Opened 7 years ago
Closed 7 years ago
#953 closed enhancement (fixed)
Remove "unmapped.bam" file from Tophat results
| Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
|---|---|---|---|
| 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)".
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(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.