[galaxy-commits] commit/galaxy-central: jgoecks: Update Cuffdiff test data to be compatible with v1.1.0

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/511941e1aea7/ changeset: 511941e1aea7 user: jgoecks date: 2011-11-18 21:14:39 summary: Update Cuffdiff test data to be compatible with v1.1.0 affected #: 11 files

diff -r 277403d31907d71e5e77694c0c97c16772f23e27 -r 511941e1aea7bcb24a1e30b1e8ac59bf0ba6a3d6 test-data/cuffdiff_out1.txt --- a/test-data/cuffdiff_out1.txt +++ b/test-data/cuffdiff_out1.txt @@ -1,99 +1,91 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value q_value significant -TCONS_00000001 XLOC_000001 - chr1:3204754-3204833 q1 q2 OK 0 5.42247e+06 1.79769e+308 1.79769e+308 0.0786496 0.550547 no -TCONS_00000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 1.39654e+08 1.79769e+308 1.79769e+308 0.158655 0.777411 no -TCONS_00000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 1.24051 no -TCONS_00000004 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 2.49256e+06 5.29759e+06 0.753941 -1.11223 0.266041 0.790061 no -TCONS_00000005 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 1.25641 no -TCONS_00000006 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 1.27273 no -TCONS_00000007 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 2.77423e+06 6.7156e+06 0.88406 -1.27269 0.203128 0.663553 no -TCONS_00000008 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 1.11098e+07 3.03942e+07 1.00642 -0.806752 0.419809 1.17547 no -TCONS_00000009 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.56023e+07 1.79769e+308 1.79769e+308 0.0416323 0.582852 no -TCONS_00000010 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 2.71123e+06 1.79769e+308 1.79769e+308 0.158655 0.598008 no -TCONS_00000011 XLOC_000014 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 1.28947 no -TCONS_00000012 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 3.93442e+06 1.79769e+308 1.79769e+308 0.0416319 0.679987 no -TCONS_00000013 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 1.39654e+08 1.79769e+308 1.79769e+308 0.158655 0.818327 no -TCONS_00000014 XLOC_000017 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 1.30667 no -TCONS_00000015 XLOC_000019 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 1.32432 no -TCONS_00000016 XLOC_000020 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 1.34247 no -TCONS_00000017 XLOC_000021 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 1.36111 no -TCONS_00000018 XLOC_000022 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 1.38028 no -TCONS_00000019 XLOC_000023 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 1.4 no -TCONS_00000020 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 460348 460348 0 0 1 1.42029 no -TCONS_00000021 XLOC_000026 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 1.44118 no -TCONS_00000022 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 37206.6 186033 1.60944 -2.18263 0.0290634 2.84821 no -TCONS_00000023 XLOC_000031 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 1.46269 no -TCONS_00000024 XLOC_000034 - chr1:3212213-3212292 q1 q2 OK 0 5.42247e+06 1.79769e+308 1.79769e+308 0.0786496 0.642305 no -TCONS_00000025 XLOC_000035 - chr1:3212367-3212439 q1 q2 OK 0 1.60978e+07 1.79769e+308 1.79769e+308 0.0416319 1.35997 no -TCONS_00000026 XLOC_000037 - chr1:3213095-3213192 q1 q2 OK 2.38694e+06 1.19347e+06 -0.693147 0.565952 0.571426 1.55555 no -TCONS_00000027 XLOC_000040 - chr1:3242633-3242923 q1 q2 OK 27029.9 243269 2.19722 -1.95282 0.0508409 0.553601 no -TCONS_00000028 XLOC_000042 - chr1:3243018-3243079 q1 q2 OK 0 1.73712e+07 1.79769e+308 1.79769e+308 0.0786496 0.700696 no -TCONS_00000029 XLOC_000044 - chr1:3243347-3243401 q1 q2 OK 0 3.32455e+07 1.79769e+308 1.79769e+308 0.0786496 0.770766 no -TCONS_00000030 XLOC_000046 - chr1:3256974-3257011 q1 q2 OK 0 1.34946e+09 1.79769e+308 1.79769e+308 0.0786496 0.481729 no -TCONS_00000031 XLOC_000048 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 1.48485 no -TCONS_00000032 XLOC_000049 - chr1:3277913-3278390 q1 q2 OK 0 0 0 0 1 1.50769 no -TCONS_00000033 XLOC_000052 - chr1:3280686-3280741 q1 q2 OK 0 1.49798e+07 1.79769e+308 1.79769e+308 0.158655 0.86379 no -TCONS_00000034 XLOC_000057 - chr1:3290488-3290553 q1 q2 OK 0 6.39146e+06 1.79769e+308 1.79769e+308 0.158655 0.676009 no -TCONS_00000035 XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 6.40392e+06 0 -1.79769e+308 -1.79769e+308 0.0814259 0.469396 no -TCONS_00000036 XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 1.2964e+06 1.46758e+06 0.124018 -0.0764318 0.939076 2.42183 no -TCONS_00000037 XLOC_000060 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 1.53125 no -TCONS_00000038 XLOC_000062 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 1.55556 no -TCONS_00000039 XLOC_000065 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 1.58065 no -TCONS_00000040 XLOC_000068 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 1 no -TCONS_00000041 XLOC_000071 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 1.01031 no -TCONS_00000042 XLOC_000073 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 1.02083 no -TCONS_00000043 XLOC_000075 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 1.03158 no -TCONS_00000044 XLOC_000077 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 1.04255 no -TCONS_00000045 XLOC_000080 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 1.05376 no -TCONS_00000046 XLOC_000083 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 1.06522 no -TCONS_00000047 XLOC_000084 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 1.07692 no -TCONS_00000048 XLOC_000085 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 1.08889 no -TCONS_00000049 XLOC_000086 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 1.10112 no -TCONS_00000050 XLOC_000087 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 1.11364 no -TCONS_00000051 XLOC_000004 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 1.12644 no -TCONS_00000052 XLOC_000005 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 1.13953 no -TCONS_00000053 XLOC_000006 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 1.15294 no -TCONS_00000054 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 171639 239968 0.335111 -1.01532 0.309956 0.893401 no -TCONS_00000055 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 227564 240951 0.0571584 -0.115428 0.908106 2.40525 no -TCONS_00000056 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 175955 319423 0.596288 -1.18662 0.235378 0.720847 no -TCONS_00000057 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 1.91712e+06 1.91712e+06 0 0 1 1.16667 no -TCONS_00000058 XLOC_000013 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 1.18072 no -TCONS_00000059 XLOC_000018 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 1.19512 no -TCONS_00000060 XLOC_000024 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 1.20988 no -TCONS_00000061 XLOC_000027 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 1.225 no -TCONS_00000062 XLOC_000028 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 2.27907 no -TCONS_00000063 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 0 0 0 0 1 2.51282 no -TCONS_00000064 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 9.11292e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 0.513844 no -TCONS_00000065 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 8.43162e+06 0 -1.79769e+308 -1.79769e+308 0.0416319 0.815985 no -TCONS_00000066 XLOC_000033 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 2.13043 no -TCONS_00000067 XLOC_000036 - chr1:3212717-3212801 q1 q2 OK 2.10791e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.647842 no -TCONS_00000068 XLOC_000038 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 2.45 no -TCONS_00000069 XLOC_000039 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 2.39024 no -TCONS_00000070 XLOC_000041 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 2.33333 no -TCONS_00000071 XLOC_000043 - chr1:3243108-3243154 q1 q2 OK 4.79961e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.740391 no -TCONS_00000072 XLOC_000045 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 2.22727 no -TCONS_00000073 XLOC_000047 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 2.17778 no -TCONS_00000074 XLOC_000049 - chr1:3277913-3278390 q1 q2 OK 127495 27320.3 -1.54045 2.07809 0.037701 1.84735 no -TCONS_00000075 XLOC_000050 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 2.08511 no -TCONS_00000076 XLOC_000051 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 2.04167 no -TCONS_00000077 XLOC_000053 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 2 no -TCONS_00000078 XLOC_000054 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 1.96 no -TCONS_00000079 XLOC_000055 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 1.92157 no -TCONS_00000080 XLOC_000056 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 1.88462 no -TCONS_00000081 XLOC_000058 - chr1:3290798-3290859 q1 q2 OK 8.68561e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.706737 no -TCONS_00000082 XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 95795.4 28263.3 -1.22065 1.20083 0.229815 0.726513 no -TCONS_00000083 XLOC_000060 - chr1:3299443-3299664 q1 q2 OK 449954 89990.7 -1.60944 1.40539 0.159905 0.540368 no -TCONS_00000084 XLOC_000061 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 1.84906 no -TCONS_00000085 XLOC_000063 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 1.81481 no -TCONS_00000086 XLOC_000064 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 1.78182 no -TCONS_00000087 XLOC_000066 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 1.75 no -TCONS_00000088 XLOC_000067 - chr1:3351240-3351311 q1 q2 OK 4.27915e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.555293 no -TCONS_00000089 XLOC_000068 - chr1:3355887-3356119 q1 q2 OK 281197 0 -1.79769e+308 -1.79769e+308 0.0416319 1.01998 no -TCONS_00000090 XLOC_000069 - chr1:3356180-3356225 q1 q2 OK 5.72196e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.57586 no -TCONS_00000091 XLOC_000070 - chr1:3363076-3363176 q1 q2 OK 2.1224e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 0.592897 no -TCONS_00000092 XLOC_000072 - chr1:3363387-3363446 q1 q2 OK 3.08417e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.509995 no -TCONS_00000093 XLOC_000074 - chr1:3364871-3364919 q1 q2 OK 3.50371e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.621929 no -TCONS_00000094 XLOC_000076 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 1.7193 no -TCONS_00000095 XLOC_000078 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 1.68966 no -TCONS_00000096 XLOC_000079 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 1.66102 no -TCONS_00000097 XLOC_000081 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 1.63333 no -TCONS_00000098 XLOC_000082 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 1.60656 no +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant +TCONS_00000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no +TCONS_00000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no +TCONS_00000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000009 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.68095e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no +TCONS_00000010 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.15515e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no +TCONS_00000011 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000012 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.02976e+06 1.79769e+308 1.79769e+308 0.0512352 0.150149 no +TCONS_00000013 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no +TCONS_00000014 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000015 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000016 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000017 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000018 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000019 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000020 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 959058 705514 -0.442943 0.376027 0.706897 1 no +TCONS_00000021 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000022 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 77513.9 285108 1.87898 -1.76152 0.0781506 1 no +TCONS_00000023 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000024 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no +TCONS_00000025 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.4671e+07 1.79769e+308 1.79769e+308 0.0512352 0.150149 no +TCONS_00000026 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 3.99739e+06 1.82908e+06 -1.12794 0.781831 0.434314 1 no +TCONS_00000027 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 56312.4 372827 2.72698 -1.67622 0.0936947 1 no +TCONS_00000028 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 2.66226e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no +TCONS_00000029 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.0951e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no +TCONS_00000030 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.06814e+09 1.79769e+308 1.79769e+308 0.0786496 0.150149 no +TCONS_00000031 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000033 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.29576e+07 1.79769e+308 1.79769e+308 0.158655 0.158655 no +TCONS_00000034 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 9.79535e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no +TCONS_00000037 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000038 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000039 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000040 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000041 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000042 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000043 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000044 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000045 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000046 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000047 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000048 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000049 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000050 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000051 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000052 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000053 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000054 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 368900 429265 0.21864 -0.483034 0.629072 1 no +TCONS_00000055 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 404373 338500 -0.25653 0.342922 0.731657 1 no +TCONS_00000056 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 402276 686974 0.772069 -1.24554 0.212932 1 no +TCONS_00000057 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 3.994e+06 2.93812e+06 -0.442943 0.217099 0.828131 1 no +TCONS_00000058 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000059 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000060 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000062 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000063 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000065 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.89853e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no +TCONS_00000066 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.31744e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.150149 no +TCONS_00000067 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000068 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 4.39147e+06 0 -1.79769e+308 -1.79769e+308 0.158655 1 no +TCONS_00000069 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 1.36901e+06 0 0 0 1 1 no +TCONS_00000070 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000071 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000072 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000073 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 9.99919e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no +TCONS_00000074 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000075 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000076 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 265614 41870.3 -2.66534 2.48499 0.0129556 1 no +TCONS_00000077 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000078 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000079 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000080 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000081 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000082 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000083 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.8095e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no +TCONS_00000084 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 342218 75524 -2.17991 1.96162 0.049807 1 no +TCONS_00000085 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 937403 137917 -2.76487 1.66807 0.0953024 1 no +TCONS_00000086 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000087 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000088 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000089 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000090 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 8.91489e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no +TCONS_00000091 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 585828 0 -1.79769e+308 -1.79769e+308 0.0512352 1 no +TCONS_00000092 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.19208e+08 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no +TCONS_00000093 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 4.42166e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 1 no +TCONS_00000094 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 4.28358e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no +TCONS_00000095 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 7.29939e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no +TCONS_00000096 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000097 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000098 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000099 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000100 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no

diff -r 277403d31907d71e5e77694c0c97c16772f23e27 -r 511941e1aea7bcb24a1e30b1e8ac59bf0ba6a3d6 test-data/cuffdiff_out10.txt --- a/test-data/cuffdiff_out10.txt +++ b/test-data/cuffdiff_out10.txt @@ -1,1 +1,88 @@ test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant +XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 FAIL 0 0 0 0 0 1 no +XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000078 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000079 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000080 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000081 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000082 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000083 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000084 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000085 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000086 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000087 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 0 1 no

diff -r 277403d31907d71e5e77694c0c97c16772f23e27 -r 511941e1aea7bcb24a1e30b1e8ac59bf0ba6a3d6 test-data/cuffdiff_out2.txt --- a/test-data/cuffdiff_out2.txt +++ b/test-data/cuffdiff_out2.txt @@ -1,88 +1,88 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value q_value significant -XLOC_000001 XLOC_000001 - chr1:3204754-3204833 q1 q2 OK 0 5.42247e+06 1.79769e+308 1.79769e+308 0.0786496 0.456168 no -XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 1.39654e+08 1.79769e+308 1.79769e+308 0.158655 0.726474 no -XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 1.8125 no -XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 1.07407 no -XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 1.12987 no -XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 1.14474 no -XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 2.6642e+06 5.53756e+06 0.731649 -1.14241 0.253284 0.734525 no -XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 227564 240951 0.0571584 -0.115428 0.908106 2.3941 no -XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 1.406e+07 3.74293e+07 0.979119 -0.979283 0.32744 0.918944 no -XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 1.91712e+06 1.91712e+06 0 0 1 1.22535 no -XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.56023e+07 1.79769e+308 1.79769e+308 0.0416323 0.452751 no -XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 2.71123e+06 1.79769e+308 1.79769e+308 0.158655 0.55212 no -XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 1.26087 no -XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 1.55357 no -XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 3.93442e+06 1.79769e+308 1.79769e+308 0.0416319 0.603662 no -XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 1.39654e+08 1.79769e+308 1.79769e+308 0.158655 0.811942 no -XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 1.52632 no -XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 1.5 no -XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 1.47458 no -XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 1.45 no -XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 1.42623 no -XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 1.40323 no -XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 1.38095 no -XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 1.35938 no -XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 460348 460348 0 0 1 1.33846 no -XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 1.31818 no -XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 1.29851 no -XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 1.27941 no -XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 37206.6 186033 1.60944 -2.18263 0.0290634 2.52852 no -XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 9.11292e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 0.488751 no -XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 1.24286 no -XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 8.43162e+06 0 -1.79769e+308 -1.79769e+308 0.0416319 0.724395 no -XLOC_000033 XLOC_000033 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 1.20833 no -XLOC_000034 XLOC_000034 - chr1:3212213-3212292 q1 q2 OK 0 5.42247e+06 1.79769e+308 1.79769e+308 0.0786496 0.526347 no -XLOC_000035 XLOC_000035 - chr1:3212367-3212439 q1 q2 OK 0 1.60978e+07 1.79769e+308 1.79769e+308 0.0416319 0.905494 no -XLOC_000036 XLOC_000036 - chr1:3212717-3212801 q1 q2 OK 2.10791e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.530885 no -XLOC_000037 XLOC_000037 - chr1:3213095-3213192 q1 q2 OK 2.38694e+06 1.19347e+06 -0.693147 0.565952 0.571426 1.55356 no -XLOC_000038 XLOC_000038 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 1.19178 no -XLOC_000039 XLOC_000039 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 1.17568 no -XLOC_000040 XLOC_000040 - chr1:3242633-3242923 q1 q2 OK 27029.9 243269 2.19722 -1.95282 0.0508409 0.491462 no -XLOC_000041 XLOC_000041 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 1.16 no -XLOC_000042 XLOC_000042 - chr1:3243018-3243079 q1 q2 OK 0 1.73712e+07 1.79769e+308 1.79769e+308 0.0786496 0.57021 no -XLOC_000043 XLOC_000043 - chr1:3243108-3243154 q1 q2 OK 4.79961e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.627409 no -XLOC_000044 XLOC_000044 - chr1:3243347-3243401 q1 q2 OK 0 3.32455e+07 1.79769e+308 1.79769e+308 0.0786496 0.622047 no -XLOC_000045 XLOC_000045 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 1.11538 no -XLOC_000046 XLOC_000046 - chr1:3256974-3257011 q1 q2 OK 0 1.34946e+09 1.79769e+308 1.79769e+308 0.0786496 0.427657 no -XLOC_000047 XLOC_000047 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 1.10127 no -XLOC_000048 XLOC_000048 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 1.0875 no -XLOC_000049 XLOC_000049 - chr1:3277913-3278390 q1 q2 OK 127495 27320.3 -1.54045 2.07809 0.037701 1.63999 no -XLOC_000050 XLOC_000050 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 1.06098 no -XLOC_000051 XLOC_000051 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 1.04819 no -XLOC_000052 XLOC_000052 - chr1:3280686-3280741 q1 q2 OK 0 1.49798e+07 1.79769e+308 1.79769e+308 0.158655 0.766834 no -XLOC_000053 XLOC_000053 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 1.03571 no -XLOC_000054 XLOC_000054 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 1.02353 no -XLOC_000055 XLOC_000055 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 1.01163 no -XLOC_000056 XLOC_000056 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 1 no -XLOC_000057 XLOC_000057 - chr1:3290488-3290553 q1 q2 OK 0 6.39146e+06 1.79769e+308 1.79769e+308 0.158655 0.69015 no -XLOC_000058 XLOC_000058 - chr1:3290798-3290859 q1 q2 OK 8.68561e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.657286 no -XLOC_000059 XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 7.79612e+06 1.49584e+06 -1.65094 1.39409 0.16329 0.48987 no -XLOC_000060 XLOC_000060 - chr1:3299443-3299664 q1 q2 OK 449954 89990.7 -1.60944 1.40539 0.159905 0.496847 no -XLOC_000061 XLOC_000061 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 2.23077 no -XLOC_000062 XLOC_000062 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 2.175 no -XLOC_000063 XLOC_000063 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 2.12195 no -XLOC_000064 XLOC_000064 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 2.07143 no -XLOC_000065 XLOC_000065 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 1.97727 no -XLOC_000066 XLOC_000066 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 1.93333 no -XLOC_000067 XLOC_000067 - chr1:3351240-3351311 q1 q2 OK 4.27915e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.600131 no -XLOC_000068 XLOC_000068 - chr1:3355887-3356119 q1 q2 OK 281197 0 -1.79769e+308 -1.79769e+308 0.0416319 1.20732 no -XLOC_000069 XLOC_000069 - chr1:3356180-3356225 q1 q2 OK 5.72196e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.575125 no -XLOC_000070 XLOC_000070 - chr1:3363076-3363176 q1 q2 OK 2.1224e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 0.684252 no -XLOC_000071 XLOC_000071 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 1.58182 no -XLOC_000072 XLOC_000072 - chr1:3363387-3363446 q1 q2 OK 3.08417e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.517429 no -XLOC_000073 XLOC_000073 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 1.61111 no -XLOC_000074 XLOC_000074 - chr1:3364871-3364919 q1 q2 OK 3.50371e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.511222 no -XLOC_000075 XLOC_000075 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 1.64151 no -XLOC_000076 XLOC_000076 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 1.67308 no -XLOC_000077 XLOC_000077 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 1.70588 no -XLOC_000078 XLOC_000078 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 1.74 no -XLOC_000079 XLOC_000079 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 1.77551 no -XLOC_000080 XLOC_000080 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 1.85106 no -XLOC_000081 XLOC_000081 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 1.8913 no -XLOC_000082 XLOC_000082 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 2.02326 no -XLOC_000083 XLOC_000083 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 2.28947 no -XLOC_000084 XLOC_000084 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 2.35135 no -XLOC_000085 XLOC_000085 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 2.41667 no -XLOC_000086 XLOC_000086 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 2.48571 no -XLOC_000087 XLOC_000087 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 2.55882 no +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant +XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.157299 no +XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.16621 no +XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 368900 429265 0.21864 -0.483034 0.629072 1 no +XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 404373 338500 -0.25653 0.342922 0.731657 1 no +XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 402276 686974 0.772069 -1.24554 0.212932 1 no +XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 3.994e+06 2.93812e+06 -0.442943 0.217099 0.828131 1 no +XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.68095e+07 1.79769e+308 1.79769e+308 0.0786496 0.157299 no +XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.15515e+06 1.79769e+308 1.79769e+308 0.158655 0.16621 no +XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.02976e+06 1.79769e+308 1.79769e+308 0.0512352 0.157299 no +XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.16621 no +XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 959058 705514 -0.442943 0.376027 0.706897 1 no +XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 77513.9 285108 1.87898 -1.76152 0.0781506 1 no +XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.89853e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.157299 no +XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.31744e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.157299 no +XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.157299 no +XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.4671e+07 1.79769e+308 1.79769e+308 0.0512352 0.157299 no +XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 4.39147e+06 0 -1.79769e+308 -1.79769e+308 0.158655 1 no +XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 5.3664e+06 1.82908e+06 -1.55284 0.839459 0.401212 0.401212 no +XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 56312.4 372827 2.72698 -1.67622 0.0936947 1 no +XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 2.66226e+07 1.79769e+308 1.79769e+308 0.0786496 0.157299 no +XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 9.99919e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no +XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.0951e+07 1.79769e+308 1.79769e+308 0.0786496 0.157299 no +XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.06814e+09 1.79769e+308 1.79769e+308 0.0786496 0.157299 no +XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 265614 41870.3 -2.66534 2.48499 0.0129556 1 no +XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.29576e+07 1.79769e+308 1.79769e+308 0.158655 0.16621 no +XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 9.79535e+06 1.79769e+308 1.79769e+308 0.158655 0.16621 no +XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.8095e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no +XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 342218 75524 -2.17991 1.96162 0.049807 1 no +XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 937403 137917 -2.76487 1.66807 0.0953024 1 no +XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 8.91489e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no +XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 585828 0 -1.79769e+308 -1.79769e+308 0.0512352 1 no +XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.19208e+08 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no +XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 4.42166e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 1 no +XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 4.28358e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.157299 no +XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 7.29939e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no +XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000078 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000079 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000080 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000081 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000082 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000083 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000084 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000085 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000086 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000087 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no

diff -r 277403d31907d71e5e77694c0c97c16772f23e27 -r 511941e1aea7bcb24a1e30b1e8ac59bf0ba6a3d6 test-data/cuffdiff_out3.txt --- a/test-data/cuffdiff_out3.txt +++ b/test-data/cuffdiff_out3.txt @@ -1,1 +1,91 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value q_value significant +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant +TSS1 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no +TSS11 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 404373 338500 -0.25653 0.342922 0.731657 1 no +TSS12 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 402276 686974 0.772069 -1.24554 0.212932 1 no +TSS15 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 3.994e+06 2.93812e+06 -0.442943 0.217099 0.828131 1 no +TSS16 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.68095e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no +TSS17 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.15515e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no +TSS18 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS19 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS2 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no +TSS20 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.02976e+06 1.79769e+308 1.79769e+308 0.0512352 0.150149 no +TSS21 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no +TSS22 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS23 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS24 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS25 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS26 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS27 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS28 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS29 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS3 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS30 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 959058 705514 -0.442943 0.376027 0.706897 1 no +TSS32 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS33 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS34 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS35 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 77513.9 285108 1.87898 -1.76152 0.0781506 1 no +TSS37 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.89853e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no +TSS38 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS39 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.31744e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.150149 no +TSS4 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS40 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS41 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no +TSS42 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.4671e+07 1.79769e+308 1.79769e+308 0.0512352 0.150149 no +TSS43 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 4.39147e+06 0 -1.79769e+308 -1.79769e+308 0.158655 1 no +TSS44 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 3.99739e+06 1.82908e+06 -1.12794 0.489836 0.62425 1 no +TSS45 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 1.36901e+06 0 0 0 1 1 no +TSS46 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS47 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS48 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 56312.4 372827 2.72698 -1.67622 0.0936947 1 no +TSS49 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS5 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS50 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 2.66226e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no +TSS51 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 9.99919e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no +TSS52 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.0951e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no +TSS53 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS54 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.06814e+09 1.79769e+308 1.79769e+308 0.0786496 0.150149 no +TSS55 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS56 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS57 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 265614 41870.3 -2.66534 2.48499 0.0129556 1 no +TSS59 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS6 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS60 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS61 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.29576e+07 1.79769e+308 1.79769e+308 0.158655 0.158655 no +TSS62 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS63 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS64 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS65 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS66 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 9.79535e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no +TSS67 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.8095e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no +TSS68 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 342218 75524 -2.17991 1.96162 0.049807 1 no +TSS7 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 368900 429265 0.21864 -0.483034 0.629072 1 no +TSS70 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 937403 137917 -2.76487 1.66807 0.0953024 1 no +TSS71 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS72 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS73 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS74 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS75 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS76 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS77 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS78 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 8.91489e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no +TSS79 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS80 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 585828 0 -1.79769e+308 -1.79769e+308 0.0512352 1 no +TSS81 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.19208e+08 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no +TSS82 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 4.42166e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 1 no +TSS83 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS84 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 4.28358e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no +TSS85 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS86 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 7.29939e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no +TSS87 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS88 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS89 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS90 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS91 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS92 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS93 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS94 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS95 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS96 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS97 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS98 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS99 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no

diff -r 277403d31907d71e5e77694c0c97c16772f23e27 -r 511941e1aea7bcb24a1e30b1e8ac59bf0ba6a3d6 test-data/cuffdiff_out4.txt --- a/test-data/cuffdiff_out4.txt +++ b/test-data/cuffdiff_out4.txt @@ -1,1 +1,1 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value q_value significant +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant

diff -r 277403d31907d71e5e77694c0c97c16772f23e27 -r 511941e1aea7bcb24a1e30b1e8ac59bf0ba6a3d6 test-data/cuffdiff_out5.txt --- a/test-data/cuffdiff_out5.txt +++ b/test-data/cuffdiff_out5.txt @@ -1,99 +1,91 @@ -tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi -TCONS_00000001 c Xkr4 XLOC_000001 - - chr1:3204754-3204833 79 - OK 0 0 0 5.42247e+06 0 1.3091e+07 -TCONS_00000002 - - XLOC_000002 - - chr1:3111449-3111490 41 - OK 0 0 0 1.39654e+08 0 4.18963e+08 -TCONS_00000003 - - XLOC_000003 - - chr1:3111545-3111576 31 - OK 0 0 0 0 0 0 -TCONS_00000004 - - XLOC_000007 - - chr1:3189810-3190789 142 - OK 2.49256e+06 0 5.08341e+06 5.29759e+06 686576 9.90861e+06 -TCONS_00000005 - - XLOC_000007 - - chr1:3189810-3190789 31 - OK 0 0 0 0 0 0 -TCONS_00000006 - - XLOC_000007 - - chr1:3189810-3190789 27 - OK 0 0 0 0 0 0 -TCONS_00000007 - - XLOC_000009 - - chr1:3191512-3192077 131 - OK 2.77423e+06 0 5.7461e+06 6.7156e+06 774909 1.26563e+07 -TCONS_00000008 - - XLOC_000009 - - chr1:3191512-3192077 69 - OK 1.11098e+07 0 3.60229e+07 3.03942e+07 0 6.3641e+07 -TCONS_00000009 - - XLOC_000011 - - chr1:3192441-3192494 53 - OK 0 0 0 5.56023e+07 0 1.19806e+08 -TCONS_00000010 - - XLOC_000012 - - chr1:3192550-3192629 79 - OK 0 0 0 2.71123e+06 0 8.1337e+06 -TCONS_00000011 - - XLOC_000014 - - chr1:3192731-3192811 80 - OK 0 0 0 0 0 0 -TCONS_00000012 - - XLOC_000015 - - chr1:3192940-3193042 102 - OK 0 0 0 3.93442e+06 0 8.47748e+06 -TCONS_00000013 - - XLOC_000016 - - chr1:3194185-3194226 41 - OK 0 0 0 1.39654e+08 0 4.18963e+08 -TCONS_00000014 - - XLOC_000017 - - chr1:3194302-3194329 27 - OK 0 0 0 0 0 0 -TCONS_00000015 - - XLOC_000019 - - chr1:3195083-3195110 27 - OK 0 0 0 0 0 0 -TCONS_00000016 - - XLOC_000020 - - chr1:3195450-3195477 27 - OK 0 0 0 0 0 0 -TCONS_00000017 - - XLOC_000021 - - chr1:3197089-3197116 27 - OK 0 0 0 0 0 0 -TCONS_00000018 - - XLOC_000022 - - chr1:3197246-3197273 27 - OK 0 0 0 0 0 0 -TCONS_00000019 - - XLOC_000023 - - chr1:3197346-3197373 27 - OK 0 0 0 0 0 0 -TCONS_00000020 - - XLOC_000025 - - chr1:3200022-3200191 169 - OK 460348 0 991912 460348 0 991912 -TCONS_00000021 - - XLOC_000026 - - chr1:3200325-3200352 27 - OK 0 0 0 0 0 0 -TCONS_00000022 - - XLOC_000029 - - chr1:3201077-3201481 404 - OK 37206.6 0 80169.2 186033 15366.6 356700 -TCONS_00000023 - - XLOC_000031 - - chr1:3201672-3201699 27 - OK 0 0 0 0 0 0 -TCONS_00000024 i Xkr4 XLOC_000034 - - chr1:3212213-3212292 79 - OK 0 0 0 5.42247e+06 0 1.3091e+07 -TCONS_00000025 i Xkr4 XLOC_000035 - - chr1:3212367-3212439 72 - OK 0 0 0 1.60978e+07 0 3.46859e+07 -TCONS_00000026 i Xkr4 XLOC_000037 - - chr1:3213095-3213192 97 - OK 2.38694e+06 0 5.76259e+06 1.19347e+06 0 3.58042e+06 -TCONS_00000027 i Xkr4 XLOC_000040 - - chr1:3242633-3242923 290 - OK 27029.9 0 81089.8 243269 0 494190 -TCONS_00000028 i Xkr4 XLOC_000042 - - chr1:3243018-3243079 61 - OK 0 0 0 1.73712e+07 0 4.19378e+07 -TCONS_00000029 i Xkr4 XLOC_000044 - - chr1:3243347-3243401 54 - OK 0 0 0 3.32455e+07 0 8.02618e+07 -TCONS_00000030 i Xkr4 XLOC_000046 - - chr1:3256974-3257011 37 - OK 0 0 0 1.34946e+09 0 3.25789e+09 -TCONS_00000031 i Xkr4 XLOC_000048 - - chr1:3277190-3277218 28 - OK 0 0 0 0 0 0 -TCONS_00000032 i Xkr4 XLOC_000049 - - chr1:3277913-3278390 27 - OK 0 0 0 0 0 0 -TCONS_00000033 i Xkr4 XLOC_000052 - - chr1:3280686-3280741 55 - OK 0 0 0 1.49798e+07 0 4.49395e+07 -TCONS_00000034 i Xkr4 XLOC_000057 - - chr1:3290488-3290553 65 - OK 0 0 0 6.39146e+06 0 1.91744e+07 -TCONS_00000035 i Xkr4 XLOC_000059 - - chr1:3290919-3291273 84 - OK 6.40392e+06 0 1.55816e+07 0 0 0 -TCONS_00000036 i Xkr4 XLOC_000059 - - chr1:3290919-3291273 98 - OK 1.2964e+06 0 4.55711e+06 1.46758e+06 0 4.47705e+06 -TCONS_00000037 i Xkr4 XLOC_000060 - - chr1:3299443-3299664 55 - OK 0 0 0 0 0 0 -TCONS_00000038 i Xkr4 XLOC_000062 - - chr1:3300051-3300078 27 - OK 0 0 0 0 0 0 -TCONS_00000039 i Xkr4 XLOC_000065 - - chr1:3318999-3319051 52 - OK 0 0 0 0 0 0 -TCONS_00000040 i Xkr4 XLOC_000068 - - chr1:3355887-3356119 27 - OK 0 0 0 0 0 0 -TCONS_00000041 i Xkr4 XLOC_000071 - - chr1:3363214-3363278 64 - OK 0 0 0 0 0 0 -TCONS_00000042 i Xkr4 XLOC_000073 - - chr1:3363753-3363849 96 - OK 0 0 0 0 0 0 -TCONS_00000043 i Xkr4 XLOC_000075 - - chr1:3367135-3367162 27 - OK 0 0 0 0 0 0 -TCONS_00000044 i Xkr4 XLOC_000077 - - chr1:3367333-3367382 49 - OK 0 0 0 0 0 0 -TCONS_00000045 i Xkr4 XLOC_000080 - - chr1:3377211-3377262 51 - OK 0 0 0 0 0 0 -TCONS_00000046 i Xkr4 XLOC_000083 - - chr1:3391325-3391352 27 - OK 0 0 0 0 0 0 -TCONS_00000047 i Xkr4 XLOC_000084 - - chr1:3435841-3435880 39 - OK 0 0 0 0 0 0 -TCONS_00000048 i Xkr4 XLOC_000085 - - chr1:3447761-3447788 27 - OK 0 0 0 0 0 0 -TCONS_00000049 i Xkr4 XLOC_000086 - - chr1:3450906-3450965 59 - OK 0 0 0 0 0 0 -TCONS_00000050 i Xkr4 XLOC_000087 - - chr1:3451051-3451109 58 - OK 0 0 0 0 0 0 -TCONS_00000051 - - XLOC_000004 - - chr1:3174765-3174792 27 - OK 0 0 0 0 0 0 -TCONS_00000052 - - XLOC_000005 - - chr1:3187401-3187428 27 - OK 0 0 0 0 0 0 -TCONS_00000053 - - XLOC_000006 - - chr1:3188521-3188548 27 - OK 0 0 0 0 0 0 -TCONS_00000054 - - XLOC_000007 - - chr1:3189810-3190789 979 - OK 171639 69105.7 274173 239968 172568 307367 -TCONS_00000055 - - XLOC_000008 - - chr1:3190858-3191434 576 - OK 227564 66605.9 388523 240951 73918.5 407983 -TCONS_00000056 - - XLOC_000009 - - chr1:3191512-3192077 565 - OK 175955 38281.8 313628 319423 117942 520904 -TCONS_00000057 - - XLOC_000010 - - chr1:3192250-3192336 86 - OK 1.91712e+06 0 5.75136e+06 1.91712e+06 0 5.75136e+06 -TCONS_00000058 - - XLOC_000013 - - chr1:3192649-3192676 27 - OK 0 0 0 0 0 0 -TCONS_00000059 - - XLOC_000018 - - chr1:3194706-3194733 27 - OK 0 0 0 0 0 0 -TCONS_00000060 - - XLOC_000024 - - chr1:3197425-3197452 27 - OK 0 0 0 0 0 0 -TCONS_00000061 - - XLOC_000027 - - chr1:3200430-3200457 27 - OK 0 0 0 0 0 0 -TCONS_00000062 - - XLOC_000028 - - chr1:3201007-3201039 32 - OK 0 0 0 0 0 0 -TCONS_00000063 - - XLOC_000029 - - chr1:3201077-3201481 27 - OK 0 0 0 0 0 0 -TCONS_00000064 - - XLOC_000030 - - chr1:3201596-3201666 70 - OK 9.11292e+06 0 2.20005e+07 0 0 0 -TCONS_00000065 - - XLOC_000032 - - chr1:3201725-3201809 84 - OK 8.43162e+06 0 1.81676e+07 0 0 0 -TCONS_00000066 i Xkr4 XLOC_000033 - - chr1:3211521-3211561 40 - OK 0 0 0 0 0 0 -TCONS_00000067 i Xkr4 XLOC_000036 - - chr1:3212717-3212801 84 - OK 2.10791e+06 0 6.32372e+06 0 0 0 -TCONS_00000068 i Xkr4 XLOC_000038 - - chr1:3240606-3240633 27 - OK 0 0 0 0 0 0 -TCONS_00000069 i Xkr4 XLOC_000039 - - chr1:3242479-3242512 33 - OK 0 0 0 0 0 0 -TCONS_00000070 i Xkr4 XLOC_000041 - - chr1:3242924-3243005 81 - OK 0 0 0 0 0 0 -TCONS_00000071 i Xkr4 XLOC_000043 - - chr1:3243108-3243154 46 - OK 4.79961e+07 0 1.43988e+08 0 0 0 -TCONS_00000072 i Xkr4 XLOC_000045 - - chr1:3254079-3254106 27 - OK 0 0 0 0 0 0 -TCONS_00000073 i Xkr4 XLOC_000047 - - chr1:3277155-3277182 27 - OK 0 0 0 0 0 0 -TCONS_00000074 i Xkr4 XLOC_000049 - - chr1:3277913-3278390 477 - OK 127495 8942.18 246048 27320.3 0 58867.2 -TCONS_00000075 i Xkr4 XLOC_000050 - - chr1:3280117-3280144 27 - OK 0 0 0 0 0 0 -TCONS_00000076 i Xkr4 XLOC_000051 - - chr1:3280498-3280525 27 - OK 0 0 0 0 0 0 -TCONS_00000077 i Xkr4 XLOC_000053 - - chr1:3282504-3282531 27 - OK 0 0 0 0 0 0 -TCONS_00000078 i Xkr4 XLOC_000054 - - chr1:3282650-3282677 27 - OK 0 0 0 0 0 0 -TCONS_00000079 i Xkr4 XLOC_000055 - - chr1:3282760-3282832 72 - OK 0 0 0 0 0 0 -TCONS_00000080 i Xkr4 XLOC_000056 - - chr1:3284966-3284993 27 - OK 0 0 0 0 0 0 -TCONS_00000081 i Xkr4 XLOC_000058 - - chr1:3290798-3290859 61 - OK 8.68561e+06 0 2.60568e+07 0 0 0 -TCONS_00000082 i Xkr4 XLOC_000059 - - chr1:3290919-3291273 354 - OK 95795.4 0 201253 28263.3 0 76569.5 -TCONS_00000083 i Xkr4 XLOC_000060 - - chr1:3299443-3299664 197 - OK 449954 0 952175 89990.7 0 269972 -TCONS_00000084 i Xkr4 XLOC_000061 - - chr1:3299691-3299733 42 - OK 0 0 0 0 0 0 -TCONS_00000085 i Xkr4 XLOC_000063 - - chr1:3307748-3307775 27 - OK 0 0 0 0 0 0 -TCONS_00000086 i Xkr4 XLOC_000064 - - chr1:3318620-3318647 27 - OK 0 0 0 0 0 0 -TCONS_00000087 i Xkr4 XLOC_000066 - - chr1:3330527-3330554 27 - OK 0 0 0 0 0 0 -TCONS_00000088 i Xkr4 XLOC_000067 - - chr1:3351240-3351311 71 - OK 4.27915e+06 0 1.28374e+07 0 0 0 -TCONS_00000089 i Xkr4 XLOC_000068 - - chr1:3355887-3356119 212 - OK 281197 0 605895 0 0 0 -TCONS_00000090 i Xkr4 XLOC_000069 - - chr1:3356180-3356225 45 - OK 5.72196e+07 0 1.71659e+08 0 0 0 -TCONS_00000091 i Xkr4 XLOC_000070 - - chr1:3363076-3363176 100 - OK 2.1224e+06 0 5.12392e+06 0 0 0 -TCONS_00000092 i Xkr4 XLOC_000072 - - chr1:3363387-3363446 59 - OK 3.08417e+07 0 6.64547e+07 0 0 0 -TCONS_00000093 i Xkr4 XLOC_000074 - - chr1:3364871-3364919 48 - OK 3.50371e+07 0 1.05111e+08 0 0 0 -TCONS_00000094 i Xkr4 XLOC_000076 - - chr1:3367210-3367237 27 - OK 0 0 0 0 0 0 -TCONS_00000095 i Xkr4 XLOC_000078 - - chr1:3369580-3369607 27 - OK 0 0 0 0 0 0 -TCONS_00000096 i Xkr4 XLOC_000079 - - chr1:3375001-3375028 27 - OK 0 0 0 0 0 0 -TCONS_00000097 i Xkr4 XLOC_000081 - - chr1:3379888-3379915 27 - OK 0 0 0 0 0 0 -TCONS_00000098 i Xkr4 XLOC_000082 - - chr1:3386739-3386836 97 - OK 0 0 0 0 0 0 +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status +TCONS_00000001 c Xkr4 XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 79 - 0 0 0 OK 8.3103e+06 0 2.00628e+07 OK +TCONS_00000002 - - XLOC_000002 - TSS2 chr1:3111449-3111490 41 - 0 0 0 OK 2.1403e+08 0 6.42089e+08 OK +TCONS_00000003 - - XLOC_000003 - TSS3 chr1:3111545-3111576 31 - 0 0 0 OK 0 0 0 OK +TCONS_00000009 - - XLOC_000011 - TSS16 chr1:3192441-3192494 53 - 0 0 0 OK 5.68095e+07 0 1.3715e+08 OK +TCONS_00000010 - - XLOC_000012 - TSS17 chr1:3192550-3192629 79 - 0 0 0 OK 4.15515e+06 0 1.24654e+07 OK +TCONS_00000011 - - XLOC_000014 - TSS19 chr1:3192731-3192811 80 - 0 0 0 OK 0 0 0 OK +TCONS_00000012 - - XLOC_000015 - TSS20 chr1:3192940-3193042 102 - 0 0 0 OK 6.02976e+06 0 1.34147e+07 OK +TCONS_00000013 - - XLOC_000016 - TSS21 chr1:3194185-3194226 41 - 0 0 0 OK 2.1403e+08 0 6.42089e+08 OK +TCONS_00000014 - - XLOC_000017 - TSS22 chr1:3194302-3194329 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000015 - - XLOC_000019 - TSS24 chr1:3195083-3195110 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000016 - - XLOC_000020 - TSS25 chr1:3195450-3195477 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000017 - - XLOC_000021 - TSS26 chr1:3197089-3197116 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000018 - - XLOC_000022 - TSS27 chr1:3197246-3197273 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000019 - - XLOC_000023 - TSS28 chr1:3197346-3197373 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000020 - - XLOC_000025 - TSS30 chr1:3200022-3200191 169 - 959058 0 2.06648e+06 OK 705514 0 1.52017e+06 OK +TCONS_00000021 - - XLOC_000026 - TSS32 chr1:3200325-3200352 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000022 - - XLOC_000029 - TSS35 chr1:3201077-3201481 404 - 77513.9 0 167019 OK 285108 21736.5 548480 OK +TCONS_00000023 - - XLOC_000031 - TSS38 chr1:3201672-3201699 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000024 i Xkr4 XLOC_000034 Xkr4 TSS41 chr1:3212213-3212292 79 - 0 0 0 OK 8.3103e+06 0 2.00628e+07 OK +TCONS_00000025 i Xkr4 XLOC_000035 Xkr4 TSS42 chr1:3212367-3212439 72 - 0 0 0 OK 2.4671e+07 0 5.48867e+07 OK +TCONS_00000026 i Xkr4 XLOC_000037 Xkr4 TSS44 chr1:3213095-3213242 97 - 3.99739e+06 3.99339e+06 4.00139e+06 LOWDATA 1.82908e+06 0 5.48723e+06 OK +TCONS_00000027 i Xkr4 XLOC_000040 Xkr4 TSS48 chr1:3242633-3242923 290 - 56312.4 0 168937 OK 372827 0 761430 OK +TCONS_00000028 i Xkr4 XLOC_000042 Xkr4 TSS50 chr1:3243018-3243079 61 - 0 0 0 OK 2.66226e+07 0 6.42725e+07 OK +TCONS_00000029 i Xkr4 XLOC_000044 Xkr4 TSS52 chr1:3243347-3243401 54 - 0 0 0 OK 5.0951e+07 0 1.23007e+08 OK +TCONS_00000030 i Xkr4 XLOC_000046 Xkr4 TSS54 chr1:3256974-3257011 37 - 0 0 0 OK 2.06814e+09 0 4.99293e+09 OK +TCONS_00000031 i Xkr4 XLOC_000048 Xkr4 TSS56 chr1:3277190-3277218 28 - 0 0 0 OK 0 0 0 OK +TCONS_00000033 i Xkr4 XLOC_000052 Xkr4 TSS61 chr1:3280686-3280741 55 - 0 0 0 OK 2.29576e+07 0 6.88728e+07 OK +TCONS_00000034 i Xkr4 XLOC_000057 Xkr4 TSS66 chr1:3290488-3290553 65 - 0 0 0 OK 9.79535e+06 0 2.9386e+07 OK +TCONS_00000037 i Xkr4 XLOC_000060 Xkr4 TSS71 chr1:3299443-3299664 55 - 0 0 0 OK 0 0 0 OK +TCONS_00000038 i Xkr4 XLOC_000062 Xkr4 TSS73 chr1:3300051-3300078 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000039 i Xkr4 XLOC_000065 Xkr4 TSS76 chr1:3318999-3319051 52 - 0 0 0 OK 0 0 0 OK +TCONS_00000040 i Xkr4 XLOC_000068 Xkr4 TSS79 chr1:3355887-3356119 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000041 i Xkr4 XLOC_000071 Xkr4 TSS83 chr1:3363214-3363278 64 - 0 0 0 OK 0 0 0 OK +TCONS_00000042 i Xkr4 XLOC_000073 Xkr4 TSS85 chr1:3363753-3363849 96 - 0 0 0 OK 0 0 0 OK +TCONS_00000043 i Xkr4 XLOC_000075 Xkr4 TSS87 chr1:3367135-3367162 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000044 i Xkr4 XLOC_000077 Xkr4 TSS89 chr1:3367333-3367382 49 - 0 0 0 OK 0 0 0 OK +TCONS_00000045 i Xkr4 XLOC_000080 Xkr4 TSS92 chr1:3377211-3377262 51 - 0 0 0 OK 0 0 0 OK +TCONS_00000046 i Xkr4 XLOC_000083 Xkr4 TSS95 chr1:3391325-3391352 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000047 i Xkr4 XLOC_000084 Xkr4 TSS96 chr1:3435841-3435880 39 - 0 0 0 OK 0 0 0 OK +TCONS_00000048 i Xkr4 XLOC_000085 Xkr4 TSS97 chr1:3447761-3447788 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000049 i Xkr4 XLOC_000086 Xkr4 TSS98 chr1:3450906-3450965 59 - 0 0 0 OK 0 0 0 OK +TCONS_00000050 i Xkr4 XLOC_000087 Xkr4 TSS99 chr1:3451051-3451109 58 - 0 0 0 OK 0 0 0 OK +TCONS_00000051 - - XLOC_000004 - TSS4 chr1:3174765-3174792 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000052 - - XLOC_000005 - TSS5 chr1:3187401-3187428 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000053 - - XLOC_000006 - TSS6 chr1:3188521-3188548 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000054 - - XLOC_000007 - TSS7 chr1:3189810-3190789 979 - 368900 151353 586447 OK 429265 337221 521309 OK +TCONS_00000055 - - XLOC_000008 - TSS11 chr1:3190858-3191434 576 - 404373 101434 707312 OK 338500 95761.5 581239 OK +TCONS_00000056 - - XLOC_000009 - TSS12 chr1:3191512-3192077 565 - 402276 96829.4 707722 OK 686974 410563 963384 OK +TCONS_00000057 - - XLOC_000010 - TSS15 chr1:3192250-3192336 86 - 3.994e+06 0 1.1982e+07 OK 2.93812e+06 0 8.81435e+06 OK +TCONS_00000058 - - XLOC_000013 - TSS18 chr1:3192649-3192676 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000059 - - XLOC_000018 - TSS23 chr1:3194706-3194733 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000060 - - XLOC_000024 - TSS29 chr1:3197425-3197452 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000062 - - XLOC_000027 - TSS33 chr1:3200430-3200457 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000063 - - XLOC_000028 - TSS34 chr1:3201007-3201039 32 - 0 0 0 OK 0 0 0 OK +TCONS_00000065 - - XLOC_000030 - TSS37 chr1:3201596-3201666 70 - 1.89853e+07 0 4.58345e+07 OK 0 0 0 OK +TCONS_00000066 - - XLOC_000032 - TSS39 chr1:3201725-3201809 84 - 1.31744e+07 0 2.83869e+07 OK 0 0 0 OK +TCONS_00000067 i Xkr4 XLOC_000033 Xkr4 TSS40 chr1:3211521-3211561 40 - 0 0 0 OK 0 0 0 OK +TCONS_00000068 i Xkr4 XLOC_000036 Xkr4 TSS43 chr1:3212717-3212801 84 - 4.39147e+06 0 1.31744e+07 OK 0 0 0 OK +TCONS_00000069 i Xkr4 XLOC_000037 Xkr4 TSS45 chr1:3213095-3213242 124 - 1.36901e+06 1.36667e+06 1.37135e+06 LOWDATA 0 0 0 OK +TCONS_00000070 i Xkr4 XLOC_000038 Xkr4 TSS46 chr1:3240606-3240633 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000071 i Xkr4 XLOC_000039 Xkr4 TSS47 chr1:3242479-3242512 33 - 0 0 0 OK 0 0 0 OK +TCONS_00000072 i Xkr4 XLOC_000041 Xkr4 TSS49 chr1:3242924-3243005 81 - 0 0 0 OK 0 0 0 OK +TCONS_00000073 i Xkr4 XLOC_000043 Xkr4 TSS51 chr1:3243108-3243154 46 - 9.99919e+07 0 2.99976e+08 OK 0 0 0 OK +TCONS_00000074 i Xkr4 XLOC_000045 Xkr4 TSS53 chr1:3254079-3254106 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000075 i Xkr4 XLOC_000047 Xkr4 TSS55 chr1:3277155-3277182 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000076 i Xkr4 XLOC_000049 Xkr4 TSS57 chr1:3277913-3278390 477 - 265614 16793 514436 OK 41870.3 0 90217.9 OK +TCONS_00000077 i Xkr4 XLOC_000050 Xkr4 TSS59 chr1:3280117-3280144 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000078 i Xkr4 XLOC_000051 Xkr4 TSS60 chr1:3280498-3280525 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000079 i Xkr4 XLOC_000053 Xkr4 TSS62 chr1:3282504-3282531 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000080 i Xkr4 XLOC_000054 Xkr4 TSS63 chr1:3282650-3282677 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000081 i Xkr4 XLOC_000055 Xkr4 TSS64 chr1:3282760-3282832 72 - 0 0 0 OK 0 0 0 OK +TCONS_00000082 i Xkr4 XLOC_000056 Xkr4 TSS65 chr1:3284966-3284993 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000083 i Xkr4 XLOC_000058 Xkr4 TSS67 chr1:3290798-3290859 61 - 1.8095e+07 0 5.4285e+07 OK 0 0 0 OK +TCONS_00000084 i Xkr4 XLOC_000059 Xkr4 TSS68 chr1:3290919-3291273 354 - 342218 0 691214 OK 75524 0 162732 OK +TCONS_00000085 i Xkr4 XLOC_000060 Xkr4 TSS70 chr1:3299443-3299664 197 - 937403 0 1.99795e+06 OK 137917 0 413751 OK +TCONS_00000086 i Xkr4 XLOC_000061 Xkr4 TSS72 chr1:3299691-3299733 42 - 0 0 0 OK 0 0 0 OK +TCONS_00000087 i Xkr4 XLOC_000063 Xkr4 TSS74 chr1:3307748-3307775 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000088 i Xkr4 XLOC_000064 Xkr4 TSS75 chr1:3318620-3318647 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000089 i Xkr4 XLOC_000066 Xkr4 TSS77 chr1:3330527-3330554 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000090 i Xkr4 XLOC_000067 Xkr4 TSS78 chr1:3351240-3351311 71 - 8.91489e+06 0 2.67447e+07 OK 0 0 0 OK +TCONS_00000091 i Xkr4 XLOC_000068 Xkr4 TSS80 chr1:3355887-3356119 212 - 585828 0 1.30332e+06 OK 0 0 0 OK +TCONS_00000092 i Xkr4 XLOC_000069 Xkr4 TSS81 chr1:3356180-3356225 45 - 1.19208e+08 0 3.57623e+08 OK 0 0 0 OK +TCONS_00000093 i Xkr4 XLOC_000070 Xkr4 TSS82 chr1:3363076-3363176 100 - 4.42166e+06 0 1.06748e+07 OK 0 0 0 OK +TCONS_00000094 i Xkr4 XLOC_000072 Xkr4 TSS84 chr1:3363387-3363446 59 - 4.28358e+07 0 1.03415e+08 OK 0 0 0 OK +TCONS_00000095 i Xkr4 XLOC_000074 Xkr4 TSS86 chr1:3364871-3364919 48 - 7.29939e+07 0 2.18982e+08 OK 0 0 0 OK +TCONS_00000096 i Xkr4 XLOC_000076 Xkr4 TSS88 chr1:3367210-3367237 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000097 i Xkr4 XLOC_000078 Xkr4 TSS90 chr1:3369580-3369607 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000098 i Xkr4 XLOC_000079 Xkr4 TSS91 chr1:3375001-3375028 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000099 i Xkr4 XLOC_000081 Xkr4 TSS93 chr1:3379888-3379915 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000100 i Xkr4 XLOC_000082 Xkr4 TSS94 chr1:3386739-3386836 97 - 0 0 0 OK 0 0 0 OK

diff -r 277403d31907d71e5e77694c0c97c16772f23e27 -r 511941e1aea7bcb24a1e30b1e8ac59bf0ba6a3d6 test-data/cuffdiff_out6.txt --- a/test-data/cuffdiff_out6.txt +++ b/test-data/cuffdiff_out6.txt @@ -1,88 +1,88 @@ -tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi -XLOC_000001 - - XLOC_000001 - - chr1:3204754-3204833 - - OK 0 0 0 5.42247e+06 0 1.3091e+07 -XLOC_000002 - - XLOC_000002 - - chr1:3111449-3111490 - - OK 0 0 0 1.39654e+08 0 4.18963e+08 -XLOC_000003 - - XLOC_000003 - - chr1:3111545-3111576 - - OK 0 0 0 0 0 0 -XLOC_000004 - - XLOC_000004 - - chr1:3174765-3174792 - - OK 0 0 0 0 0 0 -XLOC_000005 - - XLOC_000005 - - chr1:3187401-3187428 - - OK 0 0 0 0 0 0 -XLOC_000006 - - XLOC_000006 - - chr1:3188521-3188548 - - OK 0 0 0 0 0 0 -XLOC_000007 - - XLOC_000007 - - chr1:3189810-3190789 - - OK 2.6642e+06 71325.8 5.25708e+06 5.53756e+06 926051 1.01491e+07 -XLOC_000008 - - XLOC_000008 - - chr1:3190858-3191434 - - OK 227564 66605.9 388523 240951 73918.5 407983 -XLOC_000009 - - XLOC_000009 - - chr1:3191512-3192077 - - OK 1.406e+07 0 3.91501e+07 3.74293e+07 3.65533e+06 7.12032e+07 -XLOC_000010 - - XLOC_000010 - - chr1:3192250-3192336 - - OK 1.91712e+06 0 5.75136e+06 1.91712e+06 0 5.75136e+06 -XLOC_000011 - - XLOC_000011 - - chr1:3192441-3192494 - - OK 0 0 0 5.56023e+07 0 1.19806e+08 -XLOC_000012 - - XLOC_000012 - - chr1:3192550-3192629 - - OK 0 0 0 2.71123e+06 0 8.1337e+06 -XLOC_000013 - - XLOC_000013 - - chr1:3192649-3192676 - - OK 0 0 0 0 0 0 -XLOC_000014 - - XLOC_000014 - - chr1:3192731-3192811 - - OK 0 0 0 0 0 0 -XLOC_000015 - - XLOC_000015 - - chr1:3192940-3193042 - - OK 0 0 0 3.93442e+06 0 8.47748e+06 -XLOC_000016 - - XLOC_000016 - - chr1:3194185-3194226 - - OK 0 0 0 1.39654e+08 0 4.18963e+08 -XLOC_000017 - - XLOC_000017 - - chr1:3194302-3194329 - - OK 0 0 0 0 0 0 -XLOC_000018 - - XLOC_000018 - - chr1:3194706-3194733 - - OK 0 0 0 0 0 0 -XLOC_000019 - - XLOC_000019 - - chr1:3195083-3195110 - - OK 0 0 0 0 0 0 -XLOC_000020 - - XLOC_000020 - - chr1:3195450-3195477 - - OK 0 0 0 0 0 0 -XLOC_000021 - - XLOC_000021 - - chr1:3197089-3197116 - - OK 0 0 0 0 0 0 -XLOC_000022 - - XLOC_000022 - - chr1:3197246-3197273 - - OK 0 0 0 0 0 0 -XLOC_000023 - - XLOC_000023 - - chr1:3197346-3197373 - - OK 0 0 0 0 0 0 -XLOC_000024 - - XLOC_000024 - - chr1:3197425-3197452 - - OK 0 0 0 0 0 0 -XLOC_000025 - - XLOC_000025 - - chr1:3200022-3200191 - - OK 460348 0 991912 460348 0 991912 -XLOC_000026 - - XLOC_000026 - - chr1:3200325-3200352 - - OK 0 0 0 0 0 0 -XLOC_000027 - - XLOC_000027 - - chr1:3200430-3200457 - - OK 0 0 0 0 0 0 -XLOC_000028 - - XLOC_000028 - - chr1:3201007-3201039 - - OK 0 0 0 0 0 0 -XLOC_000029 - - XLOC_000029 - - chr1:3201077-3201481 - - OK 37206.6 0 80169.2 186033 15366.6 356700 -XLOC_000030 - - XLOC_000030 - - chr1:3201596-3201666 - - OK 9.11292e+06 0 2.20005e+07 0 0 0 -XLOC_000031 - - XLOC_000031 - - chr1:3201672-3201699 - - OK 0 0 0 0 0 0 -XLOC_000032 - - XLOC_000032 - - chr1:3201725-3201809 - - OK 8.43162e+06 0 1.81676e+07 0 0 0 -XLOC_000033 - - XLOC_000033 - - chr1:3211521-3211561 - - OK 0 0 0 0 0 0 -XLOC_000034 - - XLOC_000034 - - chr1:3212213-3212292 - - OK 0 0 0 5.42247e+06 0 1.3091e+07 -XLOC_000035 - - XLOC_000035 - - chr1:3212367-3212439 - - OK 0 0 0 1.60978e+07 0 3.46859e+07 -XLOC_000036 - - XLOC_000036 - - chr1:3212717-3212801 - - OK 2.10791e+06 0 6.32372e+06 0 0 0 -XLOC_000037 - - XLOC_000037 - - chr1:3213095-3213192 - - OK 2.38694e+06 0 5.76259e+06 1.19347e+06 0 3.58042e+06 -XLOC_000038 - - XLOC_000038 - - chr1:3240606-3240633 - - OK 0 0 0 0 0 0 -XLOC_000039 - - XLOC_000039 - - chr1:3242479-3242512 - - OK 0 0 0 0 0 0 -XLOC_000040 - - XLOC_000040 - - chr1:3242633-3242923 - - OK 27029.9 0 81089.8 243269 0 494190 -XLOC_000041 - - XLOC_000041 - - chr1:3242924-3243005 - - OK 0 0 0 0 0 0 -XLOC_000042 - - XLOC_000042 - - chr1:3243018-3243079 - - OK 0 0 0 1.73712e+07 0 4.19378e+07 -XLOC_000043 - - XLOC_000043 - - chr1:3243108-3243154 - - OK 4.79961e+07 0 1.43988e+08 0 0 0 -XLOC_000044 - - XLOC_000044 - - chr1:3243347-3243401 - - OK 0 0 0 3.32455e+07 0 8.02618e+07 -XLOC_000045 - - XLOC_000045 - - chr1:3254079-3254106 - - OK 0 0 0 0 0 0 -XLOC_000046 - - XLOC_000046 - - chr1:3256974-3257011 - - OK 0 0 0 1.34946e+09 0 3.25789e+09 -XLOC_000047 - - XLOC_000047 - - chr1:3277155-3277182 - - OK 0 0 0 0 0 0 -XLOC_000048 - - XLOC_000048 - - chr1:3277190-3277218 - - OK 0 0 0 0 0 0 -XLOC_000049 - - XLOC_000049 - - chr1:3277913-3278390 - - OK 127495 8942.18 246048 27320.3 0 58867.2 -XLOC_000050 - - XLOC_000050 - - chr1:3280117-3280144 - - OK 0 0 0 0 0 0 -XLOC_000051 - - XLOC_000051 - - chr1:3280498-3280525 - - OK 0 0 0 0 0 0 -XLOC_000052 - - XLOC_000052 - - chr1:3280686-3280741 - - OK 0 0 0 1.49798e+07 0 4.49395e+07 -XLOC_000053 - - XLOC_000053 - - chr1:3282504-3282531 - - OK 0 0 0 0 0 0 -XLOC_000054 - - XLOC_000054 - - chr1:3282650-3282677 - - OK 0 0 0 0 0 0 -XLOC_000055 - - XLOC_000055 - - chr1:3282760-3282832 - - OK 0 0 0 0 0 0 -XLOC_000056 - - XLOC_000056 - - chr1:3284966-3284993 - - OK 0 0 0 0 0 0 -XLOC_000057 - - XLOC_000057 - - chr1:3290488-3290553 - - OK 0 0 0 6.39146e+06 0 1.91744e+07 -XLOC_000058 - - XLOC_000058 - - chr1:3290798-3290859 - - OK 8.68561e+06 0 2.60568e+07 0 0 0 -XLOC_000059 - - XLOC_000059 - - chr1:3290919-3291273 - - OK 7.79612e+06 0 1.75364e+07 1.49584e+06 0 4.5057e+06 -XLOC_000060 - - XLOC_000060 - - chr1:3299443-3299664 - - OK 449954 0 952175 89990.7 0 269972 -XLOC_000061 - - XLOC_000061 - - chr1:3299691-3299733 - - OK 0 0 0 0 0 0 -XLOC_000062 - - XLOC_000062 - - chr1:3300051-3300078 - - OK 0 0 0 0 0 0 -XLOC_000063 - - XLOC_000063 - - chr1:3307748-3307775 - - OK 0 0 0 0 0 0 -XLOC_000064 - - XLOC_000064 - - chr1:3318620-3318647 - - OK 0 0 0 0 0 0 -XLOC_000065 - - XLOC_000065 - - chr1:3318999-3319051 - - OK 0 0 0 0 0 0 -XLOC_000066 - - XLOC_000066 - - chr1:3330527-3330554 - - OK 0 0 0 0 0 0 -XLOC_000067 - - XLOC_000067 - - chr1:3351240-3351311 - - OK 4.27915e+06 0 1.28374e+07 0 0 0 -XLOC_000068 - - XLOC_000068 - - chr1:3355887-3356119 - - OK 281197 0 605895 0 0 0 -XLOC_000069 - - XLOC_000069 - - chr1:3356180-3356225 - - OK 5.72196e+07 0 1.71659e+08 0 0 0 -XLOC_000070 - - XLOC_000070 - - chr1:3363076-3363176 - - OK 2.1224e+06 0 5.12392e+06 0 0 0 -XLOC_000071 - - XLOC_000071 - - chr1:3363214-3363278 - - OK 0 0 0 0 0 0 -XLOC_000072 - - XLOC_000072 - - chr1:3363387-3363446 - - OK 3.08417e+07 0 6.64547e+07 0 0 0 -XLOC_000073 - - XLOC_000073 - - chr1:3363753-3363849 - - OK 0 0 0 0 0 0 -XLOC_000074 - - XLOC_000074 - - chr1:3364871-3364919 - - OK 3.50371e+07 0 1.05111e+08 0 0 0 -XLOC_000075 - - XLOC_000075 - - chr1:3367135-3367162 - - OK 0 0 0 0 0 0 -XLOC_000076 - - XLOC_000076 - - chr1:3367210-3367237 - - OK 0 0 0 0 0 0 -XLOC_000077 - - XLOC_000077 - - chr1:3367333-3367382 - - OK 0 0 0 0 0 0 -XLOC_000078 - - XLOC_000078 - - chr1:3369580-3369607 - - OK 0 0 0 0 0 0 -XLOC_000079 - - XLOC_000079 - - chr1:3375001-3375028 - - OK 0 0 0 0 0 0 -XLOC_000080 - - XLOC_000080 - - chr1:3377211-3377262 - - OK 0 0 0 0 0 0 -XLOC_000081 - - XLOC_000081 - - chr1:3379888-3379915 - - OK 0 0 0 0 0 0 -XLOC_000082 - - XLOC_000082 - - chr1:3386739-3386836 - - OK 0 0 0 0 0 0 -XLOC_000083 - - XLOC_000083 - - chr1:3391325-3391352 - - OK 0 0 0 0 0 0 -XLOC_000084 - - XLOC_000084 - - chr1:3435841-3435880 - - OK 0 0 0 0 0 0 -XLOC_000085 - - XLOC_000085 - - chr1:3447761-3447788 - - OK 0 0 0 0 0 0 -XLOC_000086 - - XLOC_000086 - - chr1:3450906-3450965 - - OK 0 0 0 0 0 0 -XLOC_000087 - - XLOC_000087 - - chr1:3451051-3451109 - - OK 0 0 0 0 0 0 +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status +XLOC_000001 - - XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 - - 0 0 0 OK 8.3103e+06 0 2.00628e+07 OK +XLOC_000002 - - XLOC_000002 - TSS2 chr1:3111449-3111490 - - 0 0 0 OK 2.1403e+08 0 6.42089e+08 OK +XLOC_000003 - - XLOC_000003 - TSS3 chr1:3111545-3111576 - - 0 0 0 OK 0 0 0 OK +XLOC_000004 - - XLOC_000004 - TSS4 chr1:3174765-3174792 - - 0 0 0 OK 0 0 0 OK +XLOC_000005 - - XLOC_000005 - TSS5 chr1:3187401-3187428 - - 0 0 0 OK 0 0 0 OK +XLOC_000006 - - XLOC_000006 - TSS6 chr1:3188521-3188548 - - 0 0 0 OK 0 0 0 OK +XLOC_000007 - - XLOC_000007 - TSS7 chr1:3189810-3190789 - - 368900 151353 586447 OK 429265 337221 521309 OK +XLOC_000008 - - XLOC_000008 - TSS11 chr1:3190858-3191434 - - 404373 101434 707312 OK 338500 95761.5 581239 OK +XLOC_000009 - - XLOC_000009 - TSS12 chr1:3191512-3192077 - - 402276 96829.4 707722 OK 686974 410563 963384 OK +XLOC_000010 - - XLOC_000010 - TSS15 chr1:3192250-3192336 - - 3.994e+06 0 1.1982e+07 OK 2.93812e+06 0 8.81435e+06 OK +XLOC_000011 - - XLOC_000011 - TSS16 chr1:3192441-3192494 - - 0 0 0 OK 5.68095e+07 0 1.3715e+08 OK +XLOC_000012 - - XLOC_000012 - TSS17 chr1:3192550-3192629 - - 0 0 0 OK 4.15515e+06 0 1.24654e+07 OK +XLOC_000013 - - XLOC_000013 - TSS18 chr1:3192649-3192676 - - 0 0 0 OK 0 0 0 OK +XLOC_000014 - - XLOC_000014 - TSS19 chr1:3192731-3192811 - - 0 0 0 OK 0 0 0 OK +XLOC_000015 - - XLOC_000015 - TSS20 chr1:3192940-3193042 - - 0 0 0 OK 6.02976e+06 0 1.34147e+07 OK +XLOC_000016 - - XLOC_000016 - TSS21 chr1:3194185-3194226 - - 0 0 0 OK 2.1403e+08 0 6.42089e+08 OK +XLOC_000017 - - XLOC_000017 - TSS22 chr1:3194302-3194329 - - 0 0 0 OK 0 0 0 OK +XLOC_000018 - - XLOC_000018 - TSS23 chr1:3194706-3194733 - - 0 0 0 OK 0 0 0 OK +XLOC_000019 - - XLOC_000019 - TSS24 chr1:3195083-3195110 - - 0 0 0 OK 0 0 0 OK +XLOC_000020 - - XLOC_000020 - TSS25 chr1:3195450-3195477 - - 0 0 0 OK 0 0 0 OK +XLOC_000021 - - XLOC_000021 - TSS26 chr1:3197089-3197116 - - 0 0 0 OK 0 0 0 OK +XLOC_000022 - - XLOC_000022 - TSS27 chr1:3197246-3197273 - - 0 0 0 OK 0 0 0 OK +XLOC_000023 - - XLOC_000023 - TSS28 chr1:3197346-3197373 - - 0 0 0 OK 0 0 0 OK +XLOC_000024 - - XLOC_000024 - TSS29 chr1:3197425-3197452 - - 0 0 0 OK 0 0 0 OK +XLOC_000025 - - XLOC_000025 - TSS30 chr1:3200022-3200191 - - 959058 0 2.06648e+06 OK 705514 0 1.52017e+06 OK +XLOC_000026 - - XLOC_000026 - TSS32 chr1:3200325-3200352 - - 0 0 0 OK 0 0 0 OK +XLOC_000027 - - XLOC_000027 - TSS33 chr1:3200430-3200457 - - 0 0 0 OK 0 0 0 OK +XLOC_000028 - - XLOC_000028 - TSS34 chr1:3201007-3201039 - - 0 0 0 OK 0 0 0 OK +XLOC_000029 - - XLOC_000029 - TSS35 chr1:3201077-3201481 - - 77513.9 0 167019 OK 285108 21736.5 548480 OK +XLOC_000030 - - XLOC_000030 - TSS37 chr1:3201596-3201666 - - 1.89853e+07 0 4.58345e+07 OK 0 0 0 OK +XLOC_000031 - - XLOC_000031 - TSS38 chr1:3201672-3201699 - - 0 0 0 OK 0 0 0 OK +XLOC_000032 - - XLOC_000032 - TSS39 chr1:3201725-3201809 - - 1.31744e+07 0 2.83869e+07 OK 0 0 0 OK +XLOC_000033 - - XLOC_000033 Xkr4 TSS40 chr1:3211521-3211561 - - 0 0 0 OK 0 0 0 OK +XLOC_000034 - - XLOC_000034 Xkr4 TSS41 chr1:3212213-3212292 - - 0 0 0 OK 8.3103e+06 0 2.00628e+07 OK +XLOC_000035 - - XLOC_000035 Xkr4 TSS42 chr1:3212367-3212439 - - 0 0 0 OK 2.4671e+07 0 5.48867e+07 OK +XLOC_000036 - - XLOC_000036 Xkr4 TSS43 chr1:3212717-3212801 - - 4.39147e+06 0 1.31744e+07 OK 0 0 0 OK +XLOC_000037 - - XLOC_000037 Xkr4 TSS44,TSS45 chr1:3213095-3213242 - - 5.3664e+06 0 1.39795e+07 LOWDATA 1.82908e+06 0 5.48723e+06 OK +XLOC_000038 - - XLOC_000038 Xkr4 TSS46 chr1:3240606-3240633 - - 0 0 0 OK 0 0 0 OK +XLOC_000039 - - XLOC_000039 Xkr4 TSS47 chr1:3242479-3242512 - - 0 0 0 OK 0 0 0 OK +XLOC_000040 - - XLOC_000040 Xkr4 TSS48 chr1:3242633-3242923 - - 56312.4 0 168937 OK 372827 0 761430 OK +XLOC_000041 - - XLOC_000041 Xkr4 TSS49 chr1:3242924-3243005 - - 0 0 0 OK 0 0 0 OK +XLOC_000042 - - XLOC_000042 Xkr4 TSS50 chr1:3243018-3243079 - - 0 0 0 OK 2.66226e+07 0 6.42725e+07 OK +XLOC_000043 - - XLOC_000043 Xkr4 TSS51 chr1:3243108-3243154 - - 9.99919e+07 0 2.99976e+08 OK 0 0 0 OK +XLOC_000044 - - XLOC_000044 Xkr4 TSS52 chr1:3243347-3243401 - - 0 0 0 OK 5.0951e+07 0 1.23007e+08 OK +XLOC_000045 - - XLOC_000045 Xkr4 TSS53 chr1:3254079-3254106 - - 0 0 0 OK 0 0 0 OK +XLOC_000046 - - XLOC_000046 Xkr4 TSS54 chr1:3256974-3257011 - - 0 0 0 OK 2.06814e+09 0 4.99293e+09 OK +XLOC_000047 - - XLOC_000047 Xkr4 TSS55 chr1:3277155-3277182 - - 0 0 0 OK 0 0 0 OK +XLOC_000048 - - XLOC_000048 Xkr4 TSS56 chr1:3277190-3277218 - - 0 0 0 OK 0 0 0 OK +XLOC_000049 - - XLOC_000049 Xkr4 TSS57 chr1:3277913-3278390 - - 265614 16793 514436 OK 41870.3 0 90217.9 OK +XLOC_000050 - - XLOC_000050 Xkr4 TSS59 chr1:3280117-3280144 - - 0 0 0 OK 0 0 0 OK +XLOC_000051 - - XLOC_000051 Xkr4 TSS60 chr1:3280498-3280525 - - 0 0 0 OK 0 0 0 OK +XLOC_000052 - - XLOC_000052 Xkr4 TSS61 chr1:3280686-3280741 - - 0 0 0 OK 2.29576e+07 0 6.88728e+07 OK +XLOC_000053 - - XLOC_000053 Xkr4 TSS62 chr1:3282504-3282531 - - 0 0 0 OK 0 0 0 OK +XLOC_000054 - - XLOC_000054 Xkr4 TSS63 chr1:3282650-3282677 - - 0 0 0 OK 0 0 0 OK +XLOC_000055 - - XLOC_000055 Xkr4 TSS64 chr1:3282760-3282832 - - 0 0 0 OK 0 0 0 OK +XLOC_000056 - - XLOC_000056 Xkr4 TSS65 chr1:3284966-3284993 - - 0 0 0 OK 0 0 0 OK +XLOC_000057 - - XLOC_000057 Xkr4 TSS66 chr1:3290488-3290553 - - 0 0 0 OK 9.79535e+06 0 2.9386e+07 OK +XLOC_000058 - - XLOC_000058 Xkr4 TSS67 chr1:3290798-3290859 - - 1.8095e+07 0 5.4285e+07 OK 0 0 0 OK +XLOC_000059 - - XLOC_000059 Xkr4 TSS68 chr1:3290919-3291273 - - 342218 0 691214 OK 75524 0 162732 OK +XLOC_000060 - - XLOC_000060 Xkr4 TSS70,TSS71 chr1:3299443-3299664 - - 937403 0 1.99795e+06 OK 137917 0 413751 OK +XLOC_000061 - - XLOC_000061 Xkr4 TSS72 chr1:3299691-3299733 - - 0 0 0 OK 0 0 0 OK +XLOC_000062 - - XLOC_000062 Xkr4 TSS73 chr1:3300051-3300078 - - 0 0 0 OK 0 0 0 OK +XLOC_000063 - - XLOC_000063 Xkr4 TSS74 chr1:3307748-3307775 - - 0 0 0 OK 0 0 0 OK +XLOC_000064 - - XLOC_000064 Xkr4 TSS75 chr1:3318620-3318647 - - 0 0 0 OK 0 0 0 OK +XLOC_000065 - - XLOC_000065 Xkr4 TSS76 chr1:3318999-3319051 - - 0 0 0 OK 0 0 0 OK +XLOC_000066 - - XLOC_000066 Xkr4 TSS77 chr1:3330527-3330554 - - 0 0 0 OK 0 0 0 OK +XLOC_000067 - - XLOC_000067 Xkr4 TSS78 chr1:3351240-3351311 - - 8.91489e+06 0 2.67447e+07 OK 0 0 0 OK +XLOC_000068 - - XLOC_000068 Xkr4 TSS79,TSS80 chr1:3355887-3356119 - - 585828 0 1.30332e+06 OK 0 0 0 OK +XLOC_000069 - - XLOC_000069 Xkr4 TSS81 chr1:3356180-3356225 - - 1.19208e+08 0 3.57623e+08 OK 0 0 0 OK +XLOC_000070 - - XLOC_000070 Xkr4 TSS82 chr1:3363076-3363176 - - 4.42166e+06 0 1.06748e+07 OK 0 0 0 OK +XLOC_000071 - - XLOC_000071 Xkr4 TSS83 chr1:3363214-3363278 - - 0 0 0 OK 0 0 0 OK +XLOC_000072 - - XLOC_000072 Xkr4 TSS84 chr1:3363387-3363446 - - 4.28358e+07 0 1.03415e+08 OK 0 0 0 OK +XLOC_000073 - - XLOC_000073 Xkr4 TSS85 chr1:3363753-3363849 - - 0 0 0 OK 0 0 0 OK +XLOC_000074 - - XLOC_000074 Xkr4 TSS86 chr1:3364871-3364919 - - 7.29939e+07 0 2.18982e+08 OK 0 0 0 OK +XLOC_000075 - - XLOC_000075 Xkr4 TSS87 chr1:3367135-3367162 - - 0 0 0 OK 0 0 0 OK +XLOC_000076 - - XLOC_000076 Xkr4 TSS88 chr1:3367210-3367237 - - 0 0 0 OK 0 0 0 OK +XLOC_000077 - - XLOC_000077 Xkr4 TSS89 chr1:3367333-3367382 - - 0 0 0 OK 0 0 0 OK +XLOC_000078 - - XLOC_000078 Xkr4 TSS90 chr1:3369580-3369607 - - 0 0 0 OK 0 0 0 OK +XLOC_000079 - - XLOC_000079 Xkr4 TSS91 chr1:3375001-3375028 - - 0 0 0 OK 0 0 0 OK +XLOC_000080 - - XLOC_000080 Xkr4 TSS92 chr1:3377211-3377262 - - 0 0 0 OK 0 0 0 OK +XLOC_000081 - - XLOC_000081 Xkr4 TSS93 chr1:3379888-3379915 - - 0 0 0 OK 0 0 0 OK +XLOC_000082 - - XLOC_000082 Xkr4 TSS94 chr1:3386739-3386836 - - 0 0 0 OK 0 0 0 OK +XLOC_000083 - - XLOC_000083 Xkr4 TSS95 chr1:3391325-3391352 - - 0 0 0 OK 0 0 0 OK +XLOC_000084 - - XLOC_000084 Xkr4 TSS96 chr1:3435841-3435880 - - 0 0 0 OK 0 0 0 OK +XLOC_000085 - - XLOC_000085 Xkr4 TSS97 chr1:3447761-3447788 - - 0 0 0 OK 0 0 0 OK +XLOC_000086 - - XLOC_000086 Xkr4 TSS98 chr1:3450906-3450965 - - 0 0 0 OK 0 0 0 OK +XLOC_000087 - - XLOC_000087 Xkr4 TSS99 chr1:3451051-3451109 - - 0 0 0 OK 0 0 0 OK

diff -r 277403d31907d71e5e77694c0c97c16772f23e27 -r 511941e1aea7bcb24a1e30b1e8ac59bf0ba6a3d6 test-data/cuffdiff_out7.txt --- a/test-data/cuffdiff_out7.txt +++ b/test-data/cuffdiff_out7.txt @@ -1,1 +1,91 @@ -tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status +TSS1 - - XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 - - 0 0 0 OK 8.3103e+06 0 2.00628e+07 OK +TSS11 - - XLOC_000008 - TSS11 chr1:3190858-3191434 - - 404373 101434 707312 OK 338500 95761.5 581239 OK +TSS12 - - XLOC_000009 - TSS12 chr1:3191512-3192077 - - 402276 96829.4 707722 OK 686974 410563 963384 OK +TSS15 - - XLOC_000010 - TSS15 chr1:3192250-3192336 - - 3.994e+06 0 1.1982e+07 OK 2.93812e+06 0 8.81435e+06 OK +TSS16 - - XLOC_000011 - TSS16 chr1:3192441-3192494 - - 0 0 0 OK 5.68095e+07 0 1.3715e+08 OK +TSS17 - - XLOC_000012 - TSS17 chr1:3192550-3192629 - - 0 0 0 OK 4.15515e+06 0 1.24654e+07 OK +TSS18 - - XLOC_000013 - TSS18 chr1:3192649-3192676 - - 0 0 0 OK 0 0 0 OK +TSS19 - - XLOC_000014 - TSS19 chr1:3192731-3192811 - - 0 0 0 OK 0 0 0 OK +TSS2 - - XLOC_000002 - TSS2 chr1:3111449-3111490 - - 0 0 0 OK 2.1403e+08 0 6.42089e+08 OK +TSS20 - - XLOC_000015 - TSS20 chr1:3192940-3193042 - - 0 0 0 OK 6.02976e+06 0 1.34147e+07 OK +TSS21 - - XLOC_000016 - TSS21 chr1:3194185-3194226 - - 0 0 0 OK 2.1403e+08 0 6.42089e+08 OK +TSS22 - - XLOC_000017 - TSS22 chr1:3194302-3194329 - - 0 0 0 OK 0 0 0 OK +TSS23 - - XLOC_000018 - TSS23 chr1:3194706-3194733 - - 0 0 0 OK 0 0 0 OK +TSS24 - - XLOC_000019 - TSS24 chr1:3195083-3195110 - - 0 0 0 OK 0 0 0 OK +TSS25 - - XLOC_000020 - TSS25 chr1:3195450-3195477 - - 0 0 0 OK 0 0 0 OK +TSS26 - - XLOC_000021 - TSS26 chr1:3197089-3197116 - - 0 0 0 OK 0 0 0 OK +TSS27 - - XLOC_000022 - TSS27 chr1:3197246-3197273 - - 0 0 0 OK 0 0 0 OK +TSS28 - - XLOC_000023 - TSS28 chr1:3197346-3197373 - - 0 0 0 OK 0 0 0 OK +TSS29 - - XLOC_000024 - TSS29 chr1:3197425-3197452 - - 0 0 0 OK 0 0 0 OK +TSS3 - - XLOC_000003 - TSS3 chr1:3111545-3111576 - - 0 0 0 OK 0 0 0 OK +TSS30 - - XLOC_000025 - TSS30 chr1:3200022-3200191 - - 959058 0 2.06648e+06 OK 705514 0 1.52017e+06 OK +TSS32 - - XLOC_000026 - TSS32 chr1:3200325-3200352 - - 0 0 0 OK 0 0 0 OK +TSS33 - - XLOC_000027 - TSS33 chr1:3200430-3200457 - - 0 0 0 OK 0 0 0 OK +TSS34 - - XLOC_000028 - TSS34 chr1:3201007-3201039 - - 0 0 0 OK 0 0 0 OK +TSS35 - - XLOC_000029 - TSS35 chr1:3201077-3201481 - - 77513.9 0 167019 OK 285108 21736.5 548480 OK +TSS37 - - XLOC_000030 - TSS37 chr1:3201596-3201666 - - 1.89853e+07 0 4.58345e+07 OK 0 0 0 OK +TSS38 - - XLOC_000031 - TSS38 chr1:3201672-3201699 - - 0 0 0 OK 0 0 0 OK +TSS39 - - XLOC_000032 - TSS39 chr1:3201725-3201809 - - 1.31744e+07 0 2.83869e+07 OK 0 0 0 OK +TSS4 - - XLOC_000004 - TSS4 chr1:3174765-3174792 - - 0 0 0 OK 0 0 0 OK +TSS40 - - XLOC_000033 Xkr4 TSS40 chr1:3211521-3211561 - - 0 0 0 OK 0 0 0 OK +TSS41 - - XLOC_000034 Xkr4 TSS41 chr1:3212213-3212292 - - 0 0 0 OK 8.3103e+06 0 2.00628e+07 OK +TSS42 - - XLOC_000035 Xkr4 TSS42 chr1:3212367-3212439 - - 0 0 0 OK 2.4671e+07 0 5.48867e+07 OK +TSS43 - - XLOC_000036 Xkr4 TSS43 chr1:3212717-3212801 - - 4.39147e+06 0 1.31744e+07 OK 0 0 0 OK +TSS44 - - XLOC_000037 Xkr4 TSS44 chr1:3213095-3213242 - - 3.99739e+06 0 1.3943e+07 LOWDATA 1.82908e+06 0 5.48723e+06 OK +TSS45 - - XLOC_000037 Xkr4 TSS45 chr1:3213095-3213242 - - 1.36901e+06 0 5.30211e+06 LOWDATA 0 0 0 OK +TSS46 - - XLOC_000038 Xkr4 TSS46 chr1:3240606-3240633 - - 0 0 0 OK 0 0 0 OK +TSS47 - - XLOC_000039 Xkr4 TSS47 chr1:3242479-3242512 - - 0 0 0 OK 0 0 0 OK +TSS48 - - XLOC_000040 Xkr4 TSS48 chr1:3242633-3242923 - - 56312.4 0 168937 OK 372827 0 761430 OK +TSS49 - - XLOC_000041 Xkr4 TSS49 chr1:3242924-3243005 - - 0 0 0 OK 0 0 0 OK +TSS5 - - XLOC_000005 - TSS5 chr1:3187401-3187428 - - 0 0 0 OK 0 0 0 OK +TSS50 - - XLOC_000042 Xkr4 TSS50 chr1:3243018-3243079 - - 0 0 0 OK 2.66226e+07 0 6.42725e+07 OK +TSS51 - - XLOC_000043 Xkr4 TSS51 chr1:3243108-3243154 - - 9.99919e+07 0 2.99976e+08 OK 0 0 0 OK +TSS52 - - XLOC_000044 Xkr4 TSS52 chr1:3243347-3243401 - - 0 0 0 OK 5.0951e+07 0 1.23007e+08 OK +TSS53 - - XLOC_000045 Xkr4 TSS53 chr1:3254079-3254106 - - 0 0 0 OK 0 0 0 OK +TSS54 - - XLOC_000046 Xkr4 TSS54 chr1:3256974-3257011 - - 0 0 0 OK 2.06814e+09 0 4.99293e+09 OK +TSS55 - - XLOC_000047 Xkr4 TSS55 chr1:3277155-3277182 - - 0 0 0 OK 0 0 0 OK +TSS56 - - XLOC_000048 Xkr4 TSS56 chr1:3277190-3277218 - - 0 0 0 OK 0 0 0 OK +TSS57 - - XLOC_000049 Xkr4 TSS57 chr1:3277913-3278390 - - 265614 16793 514436 OK 41870.3 0 90217.9 OK +TSS59 - - XLOC_000050 Xkr4 TSS59 chr1:3280117-3280144 - - 0 0 0 OK 0 0 0 OK +TSS6 - - XLOC_000006 - TSS6 chr1:3188521-3188548 - - 0 0 0 OK 0 0 0 OK +TSS60 - - XLOC_000051 Xkr4 TSS60 chr1:3280498-3280525 - - 0 0 0 OK 0 0 0 OK +TSS61 - - XLOC_000052 Xkr4 TSS61 chr1:3280686-3280741 - - 0 0 0 OK 2.29576e+07 0 6.88728e+07 OK +TSS62 - - XLOC_000053 Xkr4 TSS62 chr1:3282504-3282531 - - 0 0 0 OK 0 0 0 OK +TSS63 - - XLOC_000054 Xkr4 TSS63 chr1:3282650-3282677 - - 0 0 0 OK 0 0 0 OK +TSS64 - - XLOC_000055 Xkr4 TSS64 chr1:3282760-3282832 - - 0 0 0 OK 0 0 0 OK +TSS65 - - XLOC_000056 Xkr4 TSS65 chr1:3284966-3284993 - - 0 0 0 OK 0 0 0 OK +TSS66 - - XLOC_000057 Xkr4 TSS66 chr1:3290488-3290553 - - 0 0 0 OK 9.79535e+06 0 2.9386e+07 OK +TSS67 - - XLOC_000058 Xkr4 TSS67 chr1:3290798-3290859 - - 1.8095e+07 0 5.4285e+07 OK 0 0 0 OK +TSS68 - - XLOC_000059 Xkr4 TSS68 chr1:3290919-3291273 - - 342218 0 691214 OK 75524 0 162732 OK +TSS7 - - XLOC_000007 - TSS7 chr1:3189810-3190789 - - 368900 151353 586447 OK 429265 337221 521309 OK +TSS70 - - XLOC_000060 Xkr4 TSS70 chr1:3299443-3299664 - - 937403 0 1.99795e+06 OK 137917 0 413751 OK +TSS71 - - XLOC_000060 Xkr4 TSS71 chr1:3299443-3299664 - - 0 0 0 OK 0 0 0 OK +TSS72 - - XLOC_000061 Xkr4 TSS72 chr1:3299691-3299733 - - 0 0 0 OK 0 0 0 OK +TSS73 - - XLOC_000062 Xkr4 TSS73 chr1:3300051-3300078 - - 0 0 0 OK 0 0 0 OK +TSS74 - - XLOC_000063 Xkr4 TSS74 chr1:3307748-3307775 - - 0 0 0 OK 0 0 0 OK +TSS75 - - XLOC_000064 Xkr4 TSS75 chr1:3318620-3318647 - - 0 0 0 OK 0 0 0 OK +TSS76 - - XLOC_000065 Xkr4 TSS76 chr1:3318999-3319051 - - 0 0 0 OK 0 0 0 OK +TSS77 - - XLOC_000066 Xkr4 TSS77 chr1:3330527-3330554 - - 0 0 0 OK 0 0 0 OK +TSS78 - - XLOC_000067 Xkr4 TSS78 chr1:3351240-3351311 - - 8.91489e+06 0 2.67447e+07 OK 0 0 0 OK +TSS79 - - XLOC_000068 Xkr4 TSS79 chr1:3355887-3356119 - - 0 0 0 OK 0 0 0 OK +TSS80 - - XLOC_000068 Xkr4 TSS80 chr1:3355887-3356119 - - 585828 0 1.30332e+06 OK 0 0 0 OK +TSS81 - - XLOC_000069 Xkr4 TSS81 chr1:3356180-3356225 - - 1.19208e+08 0 3.57623e+08 OK 0 0 0 OK +TSS82 - - XLOC_000070 Xkr4 TSS82 chr1:3363076-3363176 - - 4.42166e+06 0 1.06748e+07 OK 0 0 0 OK +TSS83 - - XLOC_000071 Xkr4 TSS83 chr1:3363214-3363278 - - 0 0 0 OK 0 0 0 OK +TSS84 - - XLOC_000072 Xkr4 TSS84 chr1:3363387-3363446 - - 4.28358e+07 0 1.03415e+08 OK 0 0 0 OK +TSS85 - - XLOC_000073 Xkr4 TSS85 chr1:3363753-3363849 - - 0 0 0 OK 0 0 0 OK +TSS86 - - XLOC_000074 Xkr4 TSS86 chr1:3364871-3364919 - - 7.29939e+07 0 2.18982e+08 OK 0 0 0 OK +TSS87 - - XLOC_000075 Xkr4 TSS87 chr1:3367135-3367162 - - 0 0 0 OK 0 0 0 OK +TSS88 - - XLOC_000076 Xkr4 TSS88 chr1:3367210-3367237 - - 0 0 0 OK 0 0 0 OK +TSS89 - - XLOC_000077 Xkr4 TSS89 chr1:3367333-3367382 - - 0 0 0 OK 0 0 0 OK +TSS90 - - XLOC_000078 Xkr4 TSS90 chr1:3369580-3369607 - - 0 0 0 OK 0 0 0 OK +TSS91 - - XLOC_000079 Xkr4 TSS91 chr1:3375001-3375028 - - 0 0 0 OK 0 0 0 OK +TSS92 - - XLOC_000080 Xkr4 TSS92 chr1:3377211-3377262 - - 0 0 0 OK 0 0 0 OK +TSS93 - - XLOC_000081 Xkr4 TSS93 chr1:3379888-3379915 - - 0 0 0 OK 0 0 0 OK +TSS94 - - XLOC_000082 Xkr4 TSS94 chr1:3386739-3386836 - - 0 0 0 OK 0 0 0 OK +TSS95 - - XLOC_000083 Xkr4 TSS95 chr1:3391325-3391352 - - 0 0 0 OK 0 0 0 OK +TSS96 - - XLOC_000084 Xkr4 TSS96 chr1:3435841-3435880 - - 0 0 0 OK 0 0 0 OK +TSS97 - - XLOC_000085 Xkr4 TSS97 chr1:3447761-3447788 - - 0 0 0 OK 0 0 0 OK +TSS98 - - XLOC_000086 Xkr4 TSS98 chr1:3450906-3450965 - - 0 0 0 OK 0 0 0 OK +TSS99 - - XLOC_000087 Xkr4 TSS99 chr1:3451051-3451109 - - 0 0 0 OK 0 0 0 OK

diff -r 277403d31907d71e5e77694c0c97c16772f23e27 -r 511941e1aea7bcb24a1e30b1e8ac59bf0ba6a3d6 test-data/cuffdiff_out8.txt --- a/test-data/cuffdiff_out8.txt +++ b/test-data/cuffdiff_out8.txt @@ -1,1 +1,1 @@ -tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage

diff -r 277403d31907d71e5e77694c0c97c16772f23e27 -r 511941e1aea7bcb24a1e30b1e8ac59bf0ba6a3d6 test-data/cuffdiff_out9.txt --- a/test-data/cuffdiff_out9.txt +++ b/test-data/cuffdiff_out9.txt @@ -1,1 +1,91 @@ test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant +TSS1 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS11 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS12 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS15 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS16 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS17 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS18 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS19 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS2 XLOC_000002 - chr1:3111449-3111490 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS20 XLOC_000015 - chr1:3192940-3193042 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS21 XLOC_000016 - chr1:3194185-3194226 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS22 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS23 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS24 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS25 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS26 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS27 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS28 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS29 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS3 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS30 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS32 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS33 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS34 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS35 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS37 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS38 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS39 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS4 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS40 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS41 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS42 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS43 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS44 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 FAIL 0 0 0 0 0 1 no +TSS45 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 FAIL 0 0 0 0 0 1 no +TSS46 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS47 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS48 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS49 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS5 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS50 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS51 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS52 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS53 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS54 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS55 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS56 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS57 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS59 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS6 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS60 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS61 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS62 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS63 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS64 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS65 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS66 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS67 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS68 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS7 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS70 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS71 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS72 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS73 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS74 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS75 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS76 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS77 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS78 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS79 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS80 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS81 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS82 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS83 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS84 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS85 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS86 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS87 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS88 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS89 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS90 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS91 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS92 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS93 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS94 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS95 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS96 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS97 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS98 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS99 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 0 1 no

diff -r 277403d31907d71e5e77694c0c97c16772f23e27 -r 511941e1aea7bcb24a1e30b1e8ac59bf0ba6a3d6 tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -164,7 +164,7 @@ <output name="cds_diff" file="cuffdiff_out11.txt"/><output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/><output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/> - <output name="tss_groups_exp" file="cuffdiff_out3.txt"/> + <output name="tss_groups_exp" file="cuffdiff_out3.txt" lines_diff="200"/><output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/><output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/><output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/>

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