Opened 5 weeks ago

Closed 5 weeks ago

#953 closed enhancement (fixed)

Remove "unmapped.bam" file from Tophat results

Reported by: nicklas Owned by: nicklas
Priority: major Milestone: Reggie v4.9.3
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

This file is not used anymore and just takes up space on the disk. This means that we also no longer need the tophat-recondition.py script that is doing something to "to make them compatible with downstream tools (e.g., Picard, samtools or GATK)".

Change History (1)

comment:1 Changed 5 weeks ago by nicklas

  • Resolution set to fixed
  • Status changed from new to closed

(In [4419]) Fixes #953: Remove "unmapped.bam" file from Tophat results

Remove the part of the script that calls "tophat-recondition.py". The "unmapped.bam" file is not removed until just before copying the result files back to the project archive since the "alignment_statistics.sh" script also extract some information from the unmapped.bam file.

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