Opened 5 years ago

Closed 5 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.

Change History (1)

comment:1 Changed 5 years ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed

(In [2804]) Fixes #661: Calculate average fragment size and standard deviation after tophat

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