Mercurial > repos > greg > bam_to_scidx
comparison bam_to_scidx.xml @ 1:24a8165055bd draft default tip
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author | greg |
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date | Wed, 02 Dec 2015 16:13:17 -0500 |
parents | 962b0366a980 |
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0:962b0366a980 | 1:24a8165055bd |
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23 </outputs> | 23 </outputs> |
24 <tests> | 24 <tests> |
25 <test> | 25 <test> |
26 <param name="input" value="input.bam" ftype="bam" /> | 26 <param name="input" value="input.bam" ftype="bam" /> |
27 <param name="read" value="0" /> | 27 <param name="read" value="0" /> |
28 <output name="output" file="output.scidx" /> | 28 <output name="output" file="output.scidx" lines_diff="1" /> |
29 </test> | 29 </test> |
30 </tests> | 30 </tests> |
31 <help> | 31 <help> |
32 | 32 |
33 **What it does** | 33 **What it does** |
34 | 34 |
35 Converts BAM data to ScIdx, the Strand-specific coordinate count format, which is used by | 35 Converts BAM data to ScIdx, the Strand-specific coordinate count format, which is used by tools within |
36 tools within the Chip-exo Galaxy flavor. The Chip-exo Galaxy flavor is used by the Center for | 36 the Chip-exo Galaxy flavor. ScIdx files are 1-based. The format consists of 5 columns: the chromosome, |
37 Eukaryotic Gene Regulation labs at The Pennsylvania State University. ScIdx files are 1-based. | 37 the position of the genomic coordinate, the number of tags on the forward strand, the number of tags on |
38 the reverse strand and the number of total tags on the position. With pair-end reads, only the 5’ end of | |
39 READ1 will be used to create the ScIdx data file. Tools that use this format include GeneTrack and MultiGPS. | |
38 | 40 |
39 </help> | 41 </help> |
40 <citations> | 42 <citations> |
41 <citation type="bibtex"> | 43 <citation type="bibtex"> |
42 @unpublished{None, | 44 @unpublished{None, |