Opened 10 years ago
Closed 10 years ago
#661 closed enhancement (fixed)
Calculate average fragment size and standard deviation after tophat
| Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
|---|---|---|---|
| Priority: | major | Milestone: | Reggie v2.16.2 |
| Component: | net.sf.basedb.reggie | Keywords: | |
| Cc: |
Description
This is the same as we already do in the demux step. But in this case we should use the accepted_hits.bam as source. The awk scripts work on a *.sam files though, so a conversion is needed:
samtools view accepted_hits.bam | singlecolumnaverager.awk
The result should be imported to BASE using the same annotations as before and attached to AlignedSequences items.
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(In [2804]) Fixes #661: Calculate average fragment size and standard deviation after tophat