Mercurial > repos > greg > bam_to_scidx
changeset 1:24a8165055bd draft default tip
Uploaded
| author | greg |
|---|---|
| date | Wed, 02 Dec 2015 16:13:17 -0500 |
| parents | 962b0366a980 |
| children | |
| files | bam_to_scidx.xml |
| diffstat | 1 files changed, 6 insertions(+), 4 deletions(-) [+] |
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--- a/bam_to_scidx.xml Tue Nov 24 08:13:56 2015 -0500 +++ b/bam_to_scidx.xml Wed Dec 02 16:13:17 2015 -0500 @@ -25,16 +25,18 @@ <test> <param name="input" value="input.bam" ftype="bam" /> <param name="read" value="0" /> - <output name="output" file="output.scidx" /> + <output name="output" file="output.scidx" lines_diff="1" /> </test> </tests> <help> **What it does** -Converts BAM data to ScIdx, the Strand-specific coordinate count format, which is used by -tools within the Chip-exo Galaxy flavor. The Chip-exo Galaxy flavor is used by the Center for -Eukaryotic Gene Regulation labs at The Pennsylvania State University. ScIdx files are 1-based. +Converts BAM data to ScIdx, the Strand-specific coordinate count format, which is used by tools within +the Chip-exo Galaxy flavor. ScIdx files are 1-based. The format consists of 5 columns: the chromosome, +the position of the genomic coordinate, the number of tags on the forward strand, the number of tags on +the reverse strand and the number of total tags on the position. With pair-end reads, only the 5’ end of +READ1 will be used to create the ScIdx data file. Tools that use this format include GeneTrack and MultiGPS. </help> <citations>