1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/84942418e699/ changeset: r5523:84942418e699 user: jgoecks date: 2011-05-09 18:59:42 summary: Update cuffdiff wrapper and test data for v1.0.1 affected #: 14 files (12.0 KB)
--- a/test-data/cuffdiff_out1.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out1.txt Mon May 09 12:59:42 2011 -0400 @@ -1,99 +1,99 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant -TCONS_00000001 - chr1:3204754-3204833 q1 q2 OK 0 0 0 0 1 no -TCONS_00000002 - chr1:3111449-3111490 q1 q2 OK 0 0 0 0 1 no -TCONS_00000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 no -TCONS_00000004 - chr1:3189810-3190789 q1 q2 OK 0 645918 6.95322e-310 1.79769e+308 0 yes -TCONS_00000005 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 no -TCONS_00000006 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 no -TCONS_00000007 - chr1:3191512-3192077 q1 q2 OK 0 704881 6.95322e-310 1.79769e+308 0 yes -TCONS_00000008 - chr1:3191512-3192077 q1 q2 OK 0 0 0 0 1 no -TCONS_00000009 - chr1:3192441-3192494 q1 q2 OK 0 0 0 0 1 no -TCONS_00000010 - chr1:3192550-3192629 q1 q2 OK 0 0 0 0 1 no -TCONS_00000011 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 no -TCONS_00000012 - chr1:3192940-3193042 q1 q2 OK 0 0 0 0 1 no -TCONS_00000013 - chr1:3194185-3194226 q1 q2 OK 0 0 0 0 1 no -TCONS_00000014 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 no -TCONS_00000015 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 no -TCONS_00000016 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 no -TCONS_00000017 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 no -TCONS_00000018 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 no -TCONS_00000019 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 no -TCONS_00000020 - chr1:3200022-3200191 q1 q2 OK 0 0 0 0 1 no -TCONS_00000021 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 no -TCONS_00000022 - chr1:3201077-3201481 q1 q2 OK 0 155328 0 1.79769e+308 0 yes -TCONS_00000023 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 no -TCONS_00000024 - chr1:3212213-3212292 q1 q2 OK 0 0 0 0 1 no -TCONS_00000025 - chr1:3212367-3212439 q1 q2 OK 0 0 0 0 1 no -TCONS_00000026 - chr1:3213095-3213192 q1 q2 OK 0 0 0 0 1 no -TCONS_00000027 - chr1:3242633-3242923 q1 q2 OK 0 0 0 0 1 no -TCONS_00000028 - chr1:3243018-3243079 q1 q2 OK 0 0 0 0 1 no -TCONS_00000029 - chr1:3243347-3243401 q1 q2 OK 0 0 0 0 1 no -TCONS_00000030 - chr1:3256974-3257011 q1 q2 OK 0 0 0 0 1 no -TCONS_00000031 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 no -TCONS_00000032 - chr1:3277913-3278390 q1 q2 OK 0 0 0 0 1 no -TCONS_00000033 - chr1:3280686-3280741 q1 q2 OK 0 0 0 0 1 no -TCONS_00000034 - chr1:3290488-3290553 q1 q2 OK 0 0 0 0 1 no -TCONS_00000035 - chr1:3290919-3291273 q1 q2 OK 0 0 0 0 1 no -TCONS_00000036 - chr1:3290919-3291273 q1 q2 OK 0 0 0 0 1 no -TCONS_00000037 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no -TCONS_00000038 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 no -TCONS_00000039 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 no -TCONS_00000040 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no -TCONS_00000041 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 no -TCONS_00000042 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 no -TCONS_00000043 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 no -TCONS_00000044 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 no -TCONS_00000045 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 no -TCONS_00000046 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 no -TCONS_00000047 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 no -TCONS_00000048 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 no -TCONS_00000049 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 no -TCONS_00000050 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 no -TCONS_00000051 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 no -TCONS_00000052 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 no -TCONS_00000053 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 no -TCONS_00000054 - chr1:3189810-3190789 q1 q2 OK 343500 303241 -0.124659 2.28891 0.0220846 no -TCONS_00000055 - chr1:3190858-3191434 q1 q2 OK 328433 254485 -0.255089 96.5921 0 yes -TCONS_00000056 - chr1:3191512-3192077 q1 q2 OK 345096 376320 0.0866161 -1.17079 0.241685 no -TCONS_00000057 - chr1:3192250-3192336 q1 q2 OK 0 0 0 0 1 no -TCONS_00000058 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 no -TCONS_00000059 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 no -TCONS_00000060 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 no -TCONS_00000061 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 no -TCONS_00000062 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 no -TCONS_00000063 - chr1:3201077-3201481 q1 q2 OK 0 0 0 0 1 no -TCONS_00000064 - chr1:3201596-3201666 q1 q2 OK 0 0 0 0 1 no -TCONS_00000065 - chr1:3201725-3201809 q1 q2 OK 0 0 0 0 1 no -TCONS_00000066 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 no -TCONS_00000067 - chr1:3212717-3212801 q1 q2 OK 0 0 0 0 1 no -TCONS_00000068 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 no -TCONS_00000069 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 no -TCONS_00000070 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 no -TCONS_00000071 - chr1:3243108-3243154 q1 q2 OK 0 0 0 0 1 no -TCONS_00000072 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 no -TCONS_00000073 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 no -TCONS_00000074 - chr1:3277913-3278390 q1 q2 OK 165459 0 0 2.22507e-308 0 yes -TCONS_00000075 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 no -TCONS_00000076 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 no -TCONS_00000077 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 no -TCONS_00000078 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 no -TCONS_00000079 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 no -TCONS_00000080 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 no -TCONS_00000081 - chr1:3290798-3290859 q1 q2 OK 0 0 0 0 1 no -TCONS_00000082 - chr1:3290919-3291273 q1 q2 OK 163613 0 0 2.22507e-308 0 yes -TCONS_00000083 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no -TCONS_00000084 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 no -TCONS_00000085 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 no -TCONS_00000086 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 no -TCONS_00000087 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 no -TCONS_00000088 - chr1:3351240-3351311 q1 q2 OK 0 0 0 0 1 no -TCONS_00000089 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no -TCONS_00000090 - chr1:3356180-3356225 q1 q2 OK 0 0 0 0 1 no -TCONS_00000091 - chr1:3363076-3363176 q1 q2 OK 0 0 0 0 1 no -TCONS_00000092 - chr1:3363387-3363446 q1 q2 OK 0 0 0 0 1 no -TCONS_00000093 - chr1:3364871-3364919 q1 q2 OK 0 0 0 0 1 no -TCONS_00000094 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 no -TCONS_00000095 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 no -TCONS_00000096 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 no -TCONS_00000097 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 no -TCONS_00000098 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 no +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
--- a/test-data/cuffdiff_out10.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out10.txt Mon May 09 12:59:42 2011 -0400 @@ -1,1 +1,1 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant
--- a/test-data/cuffdiff_out11.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out11.txt Mon May 09 12:59:42 2011 -0400 @@ -1,1 +1,1 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant
--- a/test-data/cuffdiff_out2.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out2.txt Mon May 09 12:59:42 2011 -0400 @@ -1,88 +1,88 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant -XLOC_000001 - chr1:3204754-3204833 q1 q2 OK 0 0 0 0 1 no -XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 0 0 0 1 no -XLOC_000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 no -XLOC_000004 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 no -XLOC_000005 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 no -XLOC_000006 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 no -XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 343500 949159 1.01639 -7.54436 4.55191e-14 yes -XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 328433 254485 -0.255089 96.5921 0 yes -XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 345096 1.0812e+06 1.142 -9.91597 0 yes -XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 0 0 0 0 1 no -XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 0 0 0 1 no -XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 0 0 0 1 no -XLOC_000013 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 no -XLOC_000014 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 no -XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 0 0 0 1 no -XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 0 0 0 1 no -XLOC_000017 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 no -XLOC_000018 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 no -XLOC_000019 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 no -XLOC_000020 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 no -XLOC_000021 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 no -XLOC_000022 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 no -XLOC_000023 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 no -XLOC_000024 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 no -XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 0 0 0 0 1 no -XLOC_000026 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 no -XLOC_000027 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 no -XLOC_000028 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 no -XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 0 155328 6.95322e-310 1.79769e+308 0 yes -XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 0 0 0 0 1 no -XLOC_000031 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 no -XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 0 0 0 0 1 no -XLOC_000033 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 no -XLOC_000034 - chr1:3212213-3212292 q1 q2 OK 0 0 0 0 1 no -XLOC_000035 - chr1:3212367-3212439 q1 q2 OK 0 0 0 0 1 no -XLOC_000036 - chr1:3212717-3212801 q1 q2 OK 0 0 0 0 1 no -XLOC_000037 - chr1:3213095-3213192 q1 q2 OK 0 0 0 0 1 no -XLOC_000038 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 no -XLOC_000039 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 no -XLOC_000040 - chr1:3242633-3242923 q1 q2 OK 0 0 0 0 1 no -XLOC_000041 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 no -XLOC_000042 - chr1:3243018-3243079 q1 q2 OK 0 0 0 0 1 no -XLOC_000043 - chr1:3243108-3243154 q1 q2 OK 0 0 0 0 1 no -XLOC_000044 - chr1:3243347-3243401 q1 q2 OK 0 0 0 0 1 no -XLOC_000045 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 no -XLOC_000046 - chr1:3256974-3257011 q1 q2 OK 0 0 0 0 1 no -XLOC_000047 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 no -XLOC_000048 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 no -XLOC_000049 - chr1:3277913-3278390 q1 q2 OK 165459 0 6.95322e-310 2.22507e-308 0 yes -XLOC_000050 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 no -XLOC_000051 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 no -XLOC_000052 - chr1:3280686-3280741 q1 q2 OK 0 0 0 0 1 no -XLOC_000053 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 no -XLOC_000054 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 no -XLOC_000055 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 no -XLOC_000056 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 no -XLOC_000057 - chr1:3290488-3290553 q1 q2 OK 0 0 0 0 1 no -XLOC_000058 - chr1:3290798-3290859 q1 q2 OK 0 0 0 0 1 no -XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 163613 0 6.95322e-310 2.22507e-308 0 yes -XLOC_000060 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no -XLOC_000061 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 no -XLOC_000062 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 no -XLOC_000063 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 no -XLOC_000064 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 no -XLOC_000065 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 no -XLOC_000066 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 no -XLOC_000067 - chr1:3351240-3351311 q1 q2 OK 0 0 0 0 1 no -XLOC_000068 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no -XLOC_000069 - chr1:3356180-3356225 q1 q2 OK 0 0 0 0 1 no -XLOC_000070 - chr1:3363076-3363176 q1 q2 OK 0 0 0 0 1 no -XLOC_000071 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 no -XLOC_000072 - chr1:3363387-3363446 q1 q2 OK 0 0 0 0 1 no -XLOC_000073 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 no -XLOC_000074 - chr1:3364871-3364919 q1 q2 OK 0 0 0 0 1 no -XLOC_000075 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 no -XLOC_000076 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 no -XLOC_000077 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 no -XLOC_000078 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 no -XLOC_000079 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 no -XLOC_000080 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 no -XLOC_000081 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 no -XLOC_000082 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 no -XLOC_000083 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 no -XLOC_000084 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 no -XLOC_000085 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 no -XLOC_000086 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 no -XLOC_000087 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 no +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
--- a/test-data/cuffdiff_out3.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out3.txt Mon May 09 12:59:42 2011 -0400 @@ -1,1 +1,1 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant +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
--- a/test-data/cuffdiff_out4.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out4.txt Mon May 09 12:59:42 2011 -0400 @@ -1,1 +1,1 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant +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
--- a/test-data/cuffdiff_out5.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out5.txt Mon May 09 12:59:42 2011 -0400 @@ -1,99 +1,99 @@ -tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi -TCONS_00000001 c Xkr4 - - chr1:3204754-3204833 0 0 0 0 0 0 -TCONS_00000002 - - - - chr1:3111449-3111490 0 0 0 0 0 0 -TCONS_00000003 - - - - chr1:3111545-3111576 0 0 0 0 0 0 -TCONS_00000004 - - - - chr1:3189810-3190789 0 0 0 645918 357201 934636 -TCONS_00000005 - - - - chr1:3189810-3190789 0 0 0 0 0 0 -TCONS_00000006 - - - - chr1:3189810-3190789 0 0 0 0 0 0 -TCONS_00000007 - - - - chr1:3191512-3192077 0 0 0 704881 400219 1.00954e+06 -TCONS_00000008 - - - - chr1:3191512-3192077 0 0 0 0 0 0 -TCONS_00000009 - - - - chr1:3192441-3192494 0 0 0 0 0 0 -TCONS_00000010 - - - - chr1:3192550-3192629 0 0 0 0 0 0 -TCONS_00000011 - - - - chr1:3192731-3192811 0 0 0 0 0 0 -TCONS_00000012 - - - - chr1:3192940-3193042 0 0 0 0 0 0 -TCONS_00000013 - - - - chr1:3194185-3194226 0 0 0 0 0 0 -TCONS_00000014 - - - - chr1:3194302-3194329 0 0 0 0 0 0 -TCONS_00000015 - - - - chr1:3195083-3195110 0 0 0 0 0 0 -TCONS_00000016 - - - - chr1:3195450-3195477 0 0 0 0 0 0 -TCONS_00000017 - - - - chr1:3197089-3197116 0 0 0 0 0 0 -TCONS_00000018 - - - - chr1:3197246-3197273 0 0 0 0 0 0 -TCONS_00000019 - - - - chr1:3197346-3197373 0 0 0 0 0 0 -TCONS_00000020 - - - - chr1:3200022-3200191 0 0 0 0 0 0 -TCONS_00000021 - - - - chr1:3200325-3200352 0 0 0 0 0 0 -TCONS_00000022 - - - - chr1:3201077-3201481 0 0 0 155328 154540 156116 -TCONS_00000023 - - - - chr1:3201672-3201699 0 0 0 0 0 0 -TCONS_00000024 i Xkr4 - - chr1:3212213-3212292 0 0 0 0 0 0 -TCONS_00000025 i Xkr4 - - chr1:3212367-3212439 0 0 0 0 0 0 -TCONS_00000026 i Xkr4 - - chr1:3213095-3213192 0 0 0 0 0 0 -TCONS_00000027 i Xkr4 - - chr1:3242633-3242923 0 0 0 0 0 0 -TCONS_00000028 i Xkr4 - - chr1:3243018-3243079 0 0 0 0 0 0 -TCONS_00000029 i Xkr4 - - chr1:3243347-3243401 0 0 0 0 0 0 -TCONS_00000030 i Xkr4 - - chr1:3256974-3257011 0 0 0 0 0 0 -TCONS_00000031 i Xkr4 - - chr1:3277190-3277218 0 0 0 0 0 0 -TCONS_00000032 i Xkr4 - - chr1:3277913-3278390 0 0 0 0 0 0 -TCONS_00000033 i Xkr4 - - chr1:3280686-3280741 0 0 0 0 0 0 -TCONS_00000034 i Xkr4 - - chr1:3290488-3290553 0 0 0 0 0 0 -TCONS_00000035 i Xkr4 - - chr1:3290919-3291273 0 0 0 0 0 0 -TCONS_00000036 i Xkr4 - - chr1:3290919-3291273 0 0 0 0 0 0 -TCONS_00000037 i Xkr4 - - chr1:3299443-3299664 0 0 0 0 0 0 -TCONS_00000038 i Xkr4 - - chr1:3300051-3300078 0 0 0 0 0 0 -TCONS_00000039 i Xkr4 - - chr1:3318999-3319051 0 0 0 0 0 0 -TCONS_00000040 i Xkr4 - - chr1:3355887-3356119 0 0 0 0 0 0 -TCONS_00000041 i Xkr4 - - chr1:3363214-3363278 0 0 0 0 0 0 -TCONS_00000042 i Xkr4 - - chr1:3363753-3363849 0 0 0 0 0 0 -TCONS_00000043 i Xkr4 - - chr1:3367135-3367162 0 0 0 0 0 0 -TCONS_00000044 i Xkr4 - - chr1:3367333-3367382 0 0 0 0 0 0 -TCONS_00000045 i Xkr4 - - chr1:3377211-3377262 0 0 0 0 0 0 -TCONS_00000046 i Xkr4 - - chr1:3391325-3391352 0 0 0 0 0 0 -TCONS_00000047 i Xkr4 - - chr1:3435841-3435880 0 0 0 0 0 0 -TCONS_00000048 i Xkr4 - - chr1:3447761-3447788 0 0 0 0 0 0 -TCONS_00000049 i Xkr4 - - chr1:3450906-3450965 0 0 0 0 0 0 -TCONS_00000050 i Xkr4 - - chr1:3451051-3451109 0 0 0 0 0 0 -TCONS_00000051 - - - - chr1:3174765-3174792 0 0 0 0 0 0 -TCONS_00000052 - - - - chr1:3187401-3187428 0 0 0 0 0 0 -TCONS_00000053 - - - - chr1:3188521-3188548 0 0 0 0 0 0 -TCONS_00000054 - - - - chr1:3189810-3190789 343500 342328 344672 303241 270227 336255 -TCONS_00000055 - - - - chr1:3190858-3191434 328433 327286 329579 254485 253476 255494 -TCONS_00000056 - - - - chr1:3191512-3192077 345096 343921 346271 376320 320653 431986 -TCONS_00000057 - - - - chr1:3192250-3192336 0 0 0 0 0 0 -TCONS_00000058 - - - - chr1:3192649-3192676 0 0 0 0 0 0 -TCONS_00000059 - - - - chr1:3194706-3194733 0 0 0 0 0 0 -TCONS_00000060 - - - - chr1:3197425-3197452 0 0 0 0 0 0 -TCONS_00000061 - - - - chr1:3200430-3200457 0 0 0 0 0 0 -TCONS_00000062 - - - - chr1:3201007-3201039 0 0 0 0 0 0 -TCONS_00000063 - - - - chr1:3201077-3201481 0 0 0 0 0 0 -TCONS_00000064 - - - - chr1:3201596-3201666 0 0 0 0 0 0 -TCONS_00000065 - - - - chr1:3201725-3201809 0 0 0 0 0 0 -TCONS_00000066 i Xkr4 - - chr1:3211521-3211561 0 0 0 0 0 0 -TCONS_00000067 i Xkr4 - - chr1:3212717-3212801 0 0 0 0 0 0 -TCONS_00000068 i Xkr4 - - chr1:3240606-3240633 0 0 0 0 0 0 -TCONS_00000069 i Xkr4 - - chr1:3242479-3242512 0 0 0 0 0 0 -TCONS_00000070 i Xkr4 - - chr1:3242924-3243005 0 0 0 0 0 0 -TCONS_00000071 i Xkr4 - - chr1:3243108-3243154 0 0 0 0 0 0 -TCONS_00000072 i Xkr4 - - chr1:3254079-3254106 0 0 0 0 0 0 -TCONS_00000073 i Xkr4 - - chr1:3277155-3277182 0 0 0 0 0 0 -TCONS_00000074 i Xkr4 - - chr1:3277913-3278390 165459 164646 166273 0 0 0 -TCONS_00000075 i Xkr4 - - chr1:3280117-3280144 0 0 0 0 0 0 -TCONS_00000076 i Xkr4 - - chr1:3280498-3280525 0 0 0 0 0 0 -TCONS_00000077 i Xkr4 - - chr1:3282504-3282531 0 0 0 0 0 0 -TCONS_00000078 i Xkr4 - - chr1:3282650-3282677 0 0 0 0 0 0 -TCONS_00000079 i Xkr4 - - chr1:3282760-3282832 0 0 0 0 0 0 -TCONS_00000080 i Xkr4 - - chr1:3284966-3284993 0 0 0 0 0 0 -TCONS_00000081 i Xkr4 - - chr1:3290798-3290859 0 0 0 0 0 0 -TCONS_00000082 i Xkr4 - - chr1:3290919-3291273 163613 162804 164422 0 0 0 -TCONS_00000083 i Xkr4 - - chr1:3299443-3299664 0 0 0 0 0 0 -TCONS_00000084 i Xkr4 - - chr1:3299691-3299733 0 0 0 0 0 0 -TCONS_00000085 i Xkr4 - - chr1:3307748-3307775 0 0 0 0 0 0 -TCONS_00000086 i Xkr4 - - chr1:3318620-3318647 0 0 0 0 0 0 -TCONS_00000087 i Xkr4 - - chr1:3330527-3330554 0 0 0 0 0 0 -TCONS_00000088 i Xkr4 - - chr1:3351240-3351311 0 0 0 0 0 0 -TCONS_00000089 i Xkr4 - - chr1:3355887-3356119 0 0 0 0 0 0 -TCONS_00000090 i Xkr4 - - chr1:3356180-3356225 0 0 0 0 0 0 -TCONS_00000091 i Xkr4 - - chr1:3363076-3363176 0 0 0 0 0 0 -TCONS_00000092 i Xkr4 - - chr1:3363387-3363446 0 0 0 0 0 0 -TCONS_00000093 i Xkr4 - - chr1:3364871-3364919 0 0 0 0 0 0 -TCONS_00000094 i Xkr4 - - chr1:3367210-3367237 0 0 0 0 0 0 -TCONS_00000095 i Xkr4 - - chr1:3369580-3369607 0 0 0 0 0 0 -TCONS_00000096 i Xkr4 - - chr1:3375001-3375028 0 0 0 0 0 0 -TCONS_00000097 i Xkr4 - - chr1:3379888-3379915 0 0 0 0 0 0 -TCONS_00000098 i Xkr4 - - chr1:3386739-3386836 0 0 0 0 0 0 +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
--- a/test-data/cuffdiff_out6.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out6.txt Mon May 09 12:59:42 2011 -0400 @@ -1,88 +1,88 @@ -tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi -XLOC_000001 - - - - chr1:3204754-3204833 0 0 0 0 0 0 -XLOC_000002 - - - - chr1:3111449-3111490 0 0 0 0 0 0 -XLOC_000003 - - - - chr1:3111545-3111576 0 0 0 0 0 0 -XLOC_000004 - - - - chr1:3174765-3174792 0 0 0 0 0 0 -XLOC_000005 - - - - chr1:3187401-3187428 0 0 0 0 0 0 -XLOC_000006 - - - - chr1:3188521-3188548 0 0 0 0 0 0 -XLOC_000007 - - - - chr1:3189810-3190789 343500 342328 344672 947555 680603 1.21451e+06 -XLOC_000008 - - - - chr1:3190858-3191434 328433 327286 329579 254485 253476 255494 -XLOC_000009 - - - - chr1:3191512-3192077 345096 343921 346271 1.07827e+06 822433 1.33412e+06 -XLOC_000010 - - - - chr1:3192250-3192336 0 0 0 0 0 0 -XLOC_000011 - - - - chr1:3192441-3192494 0 0 0 0 0 0 -XLOC_000012 - - - - chr1:3192550-3192629 0 0 0 0 0 0 -XLOC_000013 - - - - chr1:3192649-3192676 0 0 0 0 0 0 -XLOC_000014 - - - - chr1:3192731-3192811 0 0 0 0 0 0 -XLOC_000015 - - - - chr1:3192940-3193042 0 0 0 0 0 0 -XLOC_000016 - - - - chr1:3194185-3194226 0 0 0 0 0 0 -XLOC_000017 - - - - chr1:3194302-3194329 0 0 0 0 0 0 -XLOC_000018 - - - - chr1:3194706-3194733 0 0 0 0 0 0 -XLOC_000019 - - - - chr1:3195083-3195110 0 0 0 0 0 0 -XLOC_000020 - - - - chr1:3195450-3195477 0 0 0 0 0 0 -XLOC_000021 - - - - chr1:3197089-3197116 0 0 0 0 0 0 -XLOC_000022 - - - - chr1:3197246-3197273 0 0 0 0 0 0 -XLOC_000023 - - - - chr1:3197346-3197373 0 0 0 0 0 0 -XLOC_000024 - - - - chr1:3197425-3197452 0 0 0 0 0 0 -XLOC_000025 - - - - chr1:3200022-3200191 0 0 0 0 0 0 -XLOC_000026 - - - - chr1:3200325-3200352 0 0 0 0 0 0 -XLOC_000027 - - - - chr1:3200430-3200457 0 0 0 0 0 0 -XLOC_000028 - - - - chr1:3201007-3201039 0 0 0 0 0 0 -XLOC_000029 - - - - chr1:3201077-3201481 0 0 0 155328 154540 156116 -XLOC_000030 - - - - chr1:3201596-3201666 0 0 0 0 0 0 -XLOC_000031 - - - - chr1:3201672-3201699 0 0 0 0 0 0 -XLOC_000032 - - - - chr1:3201725-3201809 0 0 0 0 0 0 -XLOC_000033 - - - - chr1:3211521-3211561 0 0 0 0 0 0 -XLOC_000034 - - - - chr1:3212213-3212292 0 0 0 0 0 0 -XLOC_000035 - - - - chr1:3212367-3212439 0 0 0 0 0 0 -XLOC_000036 - - - - chr1:3212717-3212801 0 0 0 0 0 0 -XLOC_000037 - - - - chr1:3213095-3213192 0 0 0 0 0 0 -XLOC_000038 - - - - chr1:3240606-3240633 0 0 0 0 0 0 -XLOC_000039 - - - - chr1:3242479-3242512 0 0 0 0 0 0 -XLOC_000040 - - - - chr1:3242633-3242923 0 0 0 0 0 0 -XLOC_000041 - - - - chr1:3242924-3243005 0 0 0 0 0 0 -XLOC_000042 - - - - chr1:3243018-3243079 0 0 0 0 0 0 -XLOC_000043 - - - - chr1:3243108-3243154 0 0 0 0 0 0 -XLOC_000044 - - - - chr1:3243347-3243401 0 0 0 0 0 0 -XLOC_000045 - - - - chr1:3254079-3254106 0 0 0 0 0 0 -XLOC_000046 - - - - chr1:3256974-3257011 0 0 0 0 0 0 -XLOC_000047 - - - - chr1:3277155-3277182 0 0 0 0 0 0 -XLOC_000048 - - - - chr1:3277190-3277218 0 0 0 0 0 0 -XLOC_000049 - - - - chr1:3277913-3278390 165459 164646 166273 0 0 0 -XLOC_000050 - - - - chr1:3280117-3280144 0 0 0 0 0 0 -XLOC_000051 - - - - chr1:3280498-3280525 0 0 0 0 0 0 -XLOC_000052 - - - - chr1:3280686-3280741 0 0 0 0 0 0 -XLOC_000053 - - - - chr1:3282504-3282531 0 0 0 0 0 0 -XLOC_000054 - - - - chr1:3282650-3282677 0 0 0 0 0 0 -XLOC_000055 - - - - chr1:3282760-3282832 0 0 0 0 0 0 -XLOC_000056 - - - - chr1:3284966-3284993 0 0 0 0 0 0 -XLOC_000057 - - - - chr1:3290488-3290553 0 0 0 0 0 0 -XLOC_000058 - - - - chr1:3290798-3290859 0 0 0 0 0 0 -XLOC_000059 - - - - chr1:3290919-3291273 163613 162804 164422 0 0 0 -XLOC_000060 - - - - chr1:3299443-3299664 0 0 0 0 0 0 -XLOC_000061 - - - - chr1:3299691-3299733 0 0 0 0 0 0 -XLOC_000062 - - - - chr1:3300051-3300078 0 0 0 0 0 0 -XLOC_000063 - - - - chr1:3307748-3307775 0 0 0 0 0 0 -XLOC_000064 - - - - chr1:3318620-3318647 0 0 0 0 0 0 -XLOC_000065 - - - - chr1:3318999-3319051 0 0 0 0 0 0 -XLOC_000066 - - - - chr1:3330527-3330554 0 0 0 0 0 0 -XLOC_000067 - - - - chr1:3351240-3351311 0 0 0 0 0 0 -XLOC_000068 - - - - chr1:3355887-3356119 0 0 0 0 0 0 -XLOC_000069 - - - - chr1:3356180-3356225 0 0 0 0 0 0 -XLOC_000070 - - - - chr1:3363076-3363176 0 0 0 0 0 0 -XLOC_000071 - - - - chr1:3363214-3363278 0 0 0 0 0 0 -XLOC_000072 - - - - chr1:3363387-3363446 0 0 0 0 0 0 -XLOC_000073 - - - - chr1:3363753-3363849 0 0 0 0 0 0 -XLOC_000074 - - - - chr1:3364871-3364919 0 0 0 0 0 0 -XLOC_000075 - - - - chr1:3367135-3367162 0 0 0 0 0 0 -XLOC_000076 - - - - chr1:3367210-3367237 0 0 0 0 0 0 -XLOC_000077 - - - - chr1:3367333-3367382 0 0 0 0 0 0 -XLOC_000078 - - - - chr1:3369580-3369607 0 0 0 0 0 0 -XLOC_000079 - - - - chr1:3375001-3375028 0 0 0 0 0 0 -XLOC_000080 - - - - chr1:3377211-3377262 0 0 0 0 0 0 -XLOC_000081 - - - - chr1:3379888-3379915 0 0 0 0 0 0 -XLOC_000082 - - - - chr1:3386739-3386836 0 0 0 0 0 0 -XLOC_000083 - - - - chr1:3391325-3391352 0 0 0 0 0 0 -XLOC_000084 - - - - chr1:3435841-3435880 0 0 0 0 0 0 -XLOC_000085 - - - - chr1:3447761-3447788 0 0 0 0 0 0 -XLOC_000086 - - - - chr1:3450906-3450965 0 0 0 0 0 0 -XLOC_000087 - - - - chr1:3451051-3451109 0 0 0 0 0 0 +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
--- a/test-data/cuffdiff_out7.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out7.txt Mon May 09 12:59:42 2011 -0400 @@ -1,1 +1,1 @@ -tracking_id class_code nearest_ref_id gene_short_name tss_id locus +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status
--- a/test-data/cuffdiff_out8.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out8.txt Mon May 09 12:59:42 2011 -0400 @@ -1,1 +1,1 @@ -tracking_id class_code nearest_ref_id gene_short_name tss_id locus +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status
--- a/test-data/cuffdiff_out9.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out9.txt Mon May 09 12:59:42 2011 -0400 @@ -1,1 +1,1 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant
--- a/tools/ngs_rna/cuffdiff_wrapper.py Mon May 09 11:13:42 2011 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.py Mon May 09 12:59:42 2011 -0400 @@ -57,7 +57,6 @@ parser.add_option( '-m', '--inner-mean-dist', dest='inner_mean_dist', help='This is the expected (mean) inner distance between mate pairs. \ For, example, for paired end runs with fragments selected at 300bp, \ where each end is 50bp, you should set -r to be 200. The default is 45bp.') - parser.add_option( '-Q', '--min-mapqual', dest='min_mapqual', help='Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0.' ) parser.add_option( '-c', '--min-alignment-count', dest='min_alignment_count', help='The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not signficant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads).' ) parser.add_option( '--FDR', dest='FDR', help='The allowed false discovery rate. The default is 0.05.' )
@@ -78,7 +77,7 @@ parser.add_option( "-N", "--quartile-normalization", dest="do_normalization", action="store_true" )
# Bias correction options. - parser.add_option( '-r', dest='do_bias_correction', action="store_true", help='Providing Cufflinks with a multifasta file via this option instructs it to run our new bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates.') + parser.add_option( '-b', dest='do_bias_correction', action="store_true", help='Providing Cufflinks with a multifasta file via this option instructs it to run our new bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates.') parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) @@ -145,8 +144,6 @@ cmd += ( " -p %i" % int ( options.num_threads ) ) if options.inner_mean_dist: cmd += ( " -m %i" % int ( options.inner_mean_dist ) ) - if options.min_mapqual: - cmd += ( " -Q %i" % int ( options.min_mapqual ) ) if options.min_alignment_count: cmd += ( " -c %i" % int ( options.min_alignment_count ) ) if options.FDR: @@ -158,7 +155,7 @@ if options.do_normalization: cmd += ( " -N" ) if options.do_bias_correction: - cmd += ( " -r %s" % seq_path ) + cmd += ( " -b %s" % seq_path )
# Add inputs. # For replicate analysis: group1_rep1,group1_rep2 groupN_rep1,groupN_rep2
--- a/tools/ngs_rna/cuffdiff_wrapper.xml Mon May 09 11:13:42 2011 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Mon May 09 12:59:42 2011 -0400 @@ -7,7 +7,6 @@ cuffdiff_wrapper.py --FDR=$fdr --num-threads="4" - --min-mapqual=$min_mapqual --min-alignment-count=$min_alignment_count
--isoforms_fpkm_tracking_output=$isoforms_fpkm_tracking @@ -36,7 +35,7 @@
## Bias correction? #if $bias_correction.do_bias_correction == "Yes": - -r + -b #if $bias_correction.seq_source.index_source == "history": --ref_file=$bias_correction.seq_source.ref_file #else: @@ -97,7 +96,6 @@ </conditional><param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/> - <param name="min_mapqual" type="integer" value="0" label="Min SAM Mapping Quality" help="Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number."/><param name="min_alignment_count" type="integer" value="1000" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/><param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts."><option value="No">No</option> @@ -169,8 +167,8 @@ Line diffs are needed because cuffdiff does not produce deterministic output. TODO: can we find datasets that lead to deterministic behavior? --> - <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="14"/> - <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="10"/> + <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="56"/> + <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="30"/><output name="tss_groups_exp" file="cuffdiff_out3.txt"/><output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/><output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="16"/> @@ -238,7 +236,6 @@
-m INT This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 45bp. -s INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp. - -Q Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0. -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads). --FDR FLOAT The allowed false discovery rate. The default is 0.05. --num-importance-samples INT Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000
--- a/tools/ngs_rna/cufflinks_wrapper.xml Mon May 09 11:13:42 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Mon May 09 12:59:42 2011 -0400 @@ -209,7 +209,6 @@ -I INT The minimum intron length. Cufflinks will not report transcripts with introns longer than this, and will ignore SAM alignments with REF_SKIP CIGAR operations longer than this. The default is 300,000. -F After calculating isoform abundance for a gene, Cufflinks filters out transcripts that it believes are very low abundance, because isoforms expressed at extremely low levels often cannot reliably be assembled, and may even be artifacts of incompletely spliced precursors of processed transcripts. This parameter is also used to filter out introns that have far fewer spliced alignments supporting them. The default is 0.05, or 5% of the most abundant isoform (the major isoform) of the gene. -j Some RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored. The default is 5%. - -Q Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0. -G Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript. -N With this option, Cufflinks excludes the contribution of the top 25 percent most highly expressed genes from the number of mapped fragments used in the FPKM denominator. This can improve robustness of differential expression calls for less abundant genes and transcripts. </help>
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