Opened 10 years ago
Last modified 10 years ago
#658 closed enhancement
Adjust fragment size mean and standard deviation — at Initial Version
| Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
|---|---|---|---|
| Priority: | critical | Milestone: | Reggie v2.16.1 |
| Component: | net.sf.basedb.reggie | Keywords: | |
| Cc: |
Description
In the demux step we introduced a call to bowtie that is used to calculate the average fragment size and standard deviation (see [2680]). The values are used as input to Tophat for -mate-inner-dist and --mate-std-dev (see [2684]).
But after alignment Tophat reports values which are typically 13 (inner-dist) and 10 (std-dev) higher. Adjusting the input parameters with this amount gives higher alignment rate.
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