1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/83434eb47d58/ changeset: 83434eb47d58 user: inithello date: 2012-09-04 16:15:18 summary: Fixed error in solid2fasta.xml preventing help text from displaying. affected #: 1 file diff -r b31863f9408d082a8dbd209af1eb4b8609faa9ac -r 83434eb47d587fe729252fe9d7ef6e34e499afb8 tools/next_gen_conversion/solid2fastq.xml --- a/tools/next_gen_conversion/solid2fastq.xml +++ b/tools/next_gen_conversion/solid2fastq.xml @@ -66,7 +66,6 @@ </test></tests><help> - **What it does** Converts output of SOLiD instrument (versions 3.5 and earlier) to fastq format suitable for bowtie, bwa, and PerM mappers. @@ -79,22 +78,22 @@ Reads:: - >1831_573_1004_F3 + >1831_573_1004_F3 T00030133312212111300011021310132222 - >1831_573_1567_F3 + >1831_573_1567_F3 T03330322230322112131010221102122113 Quality scores:: - >1831_573_1004_F3 + >1831_573_1004_F3 4 29 34 34 32 32 24 24 20 17 10 34 29 20 34 13 30 34 22 24 11 28 19 17 34 17 24 17 25 34 7 24 14 12 22 - >1831_573_1567_F3 + >1831_573_1567_F3 8 26 31 31 16 22 30 31 28 29 22 30 30 31 32 23 30 28 28 31 19 32 30 32 19 8 32 10 13 6 32 10 6 16 11 **Mate pairs** -If your data is from a mate-paired run, you will have additional read and quality datasets that will look similar to the ones above with one exception: the names of reads will be ending with "_R3". +If your data is from a mate-paired run, you will have additional read and quality datasets that will look similar to the ones above with one exception: the names of reads will be ending with "_R3". In this case choose **Yes** from the *Is this a mate-pair run?* drop down and you will be able to select R reads. When processing mate pairs this tool generates two output files: one for F3 reads and the other for R3 reads. The reads are guaranteed to be paired -- mated reads will be in the same position in F3 and R3 fastq file. However, because pairing is verified it may take a while to process an entire SOLiD run (several hours). @@ -104,11 +103,11 @@ **Remove reads containing color qualities below this value** - any read that contains as least one color call with quality lower than the specified value **will not** be reported. -**Trim trailing "_F3" and "_R3"?** - does just that. Not necessary for bowtie. Required for BWA. +**Trim trailing "_F3" and "_R3"?** - does just that. Not necessary for bowtie. Required for BWA. **Trim first base?** - SOLiD reads contain an adapter base such as the first T in this read:: - >1831_573_1004_F3 + >1831_573_1004_F3 T00030133312212111300011021310132222 this option removes this base leaving only color calls. Not necessary for bowtie. Required for BWA. @@ -119,42 +118,37 @@ **Examples of output** -When all parameters are left "as-is" you will get this (using reads and qualities shown above):: +When all parameters are left "as-is" you will get this (using reads and qualities shown above):: @1831_573_1004 T00030133312212111300011021310132222 + - %>CCAA9952+C>5C.?C79,=42C292:C(9/-7 + %%>CCAA9952+C>5C.?C79,=42C292:C(9/-7 @1831_573_1004 T03330322230322112131010221102122113 + - );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1, + );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1, Setting *Trim first base from reads* to **Yes** will produce this:: @1831_573_1004 00030133312212111300011021310132222 + - %>CCAA9952+C>5C.?C79,=42C292:C(9/-7 + %%>CCAA9952+C>5C.?C79,=42C292:C(9/-7 @1831_573_1004 03330322230322112131010221102122113 + - );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1, + );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1, Finally, setting *Double encode* to **Yes** will yield:: @1831_573_1004 TAAATACTTTCGGCGCCCTAAACCAGCTCACTGGGG + - %>CCAA9952+C>5C.?C79,=42C292:C(9/-7 + %%>CCAA9952+C>5C.?C79,=42C292:C(9/-7 @1831_573_1004 TATTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT + - );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1, - - - - - + );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1, </help></tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.