Mercurial > repos > bgruening > deeptools
comparison bamCompare.xml @ 9:c53a73b8eef9 draft
Uploaded
| author | bgruening |
|---|---|
| date | Tue, 10 Dec 2013 12:13:18 -0500 |
| parents | d957e25e18a3 |
| children | 135f3bae5c56 |
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| 8:1c5ed9126db6 | 9:c53a73b8eef9 |
|---|---|
| 68 | 68 |
| 69 <inputs> | 69 <inputs> |
| 70 <param name="bamFile1" format="bam" type="data" label="Treatment BAM file" | 70 <param name="bamFile1" format="bam" type="data" label="Treatment BAM file" |
| 71 help="The BAM file must be sorted."/> | 71 help="The BAM file must be sorted."/> |
| 72 | 72 |
| 73 <param name="bamFile2" format="bam" type="data" label="Input BAM file" | 73 <param name="bamFile2" format="bam" type="data" label="BAM file" |
| 74 help="The BAM file must be sorted."/> | 74 help="The BAM file must be sorted."/> |
| 75 | 75 |
| 76 <param name="fragmentLength" type="integer" value="300" min="1" | 76 <param name="fragmentLength" type="integer" value="300" min="1" |
| 77 label="Length of the average fragment size" | 77 label="Length of the average fragment size" |
| 78 help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see "normalize coverage to 1x"). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/> | 78 help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see "normalize coverage to 1x"). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/> |