Closed pamelarussell closed 7 years ago
Chris7
commented
8 years ago Cutadapt is also used for other functions that aren't adapter related such as filtering based on QC and returning the phred of the input. It needs to be run for these measures. If you have done all that preprocessing yourself, a 'skip' flag I think may be more appropriate than using --adapter none
alexbaras
commented
8 years ago like chris said,
in trim_file.py we do more with cutadapt even if adapter is none
i think we can just the none flag for now
-Alex
From: pamelarussell notifications@github.com Sent: Wednesday, September 21, 2016 11:21 AM To: BarasLab/miRge Subject: [BarasLab/miRge] Bypass Cutadapt step when adapter option is "none" (#9)
Added code to skip the Cutadapt step when adapter command line option is "none". As the Cutadapt step also counts the raw and trimmed reads, added a subroutine to store these counts without running Cutadapt. Also fixed seqLibs path to reflect directory structure in current miRge.seqLibs.tar.gz.
You can view, comment on, or merge this pull request online at:
https://github.com/BarasLab/miRge/pull/9
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pamelarussell
commented
8 years ago Hi Alex and Chris,
Thanks for the comments. I pushed a new version with a --skipClipFilter option that bypasses Cutadapt, but still computes the metrics (read counts and phred). Without this option, adapter=none still causes Cutadapt to be run for filtering purposes. The "skip" feature is cutting run times by a factor of >5 for my clipped, filtered data. I also reverted the path of $refPath now that the .tar.gz has been fixed. Thanks for considering.
-Pam
Added code to skip the Cutadapt step when adapter command line option is "none". As the Cutadapt step also counts the raw and trimmed reads, added a subroutine to store these counts without running Cutadapt. Also fixed seqLibs path to reflect directory structure in current miRge.seqLibs.tar.gz.