Changes between Version 14 and Version 15 of SOPs/SAMBAMqc


Ignore:
Timestamp:
01/17/17 11:11:40 (8 years ago)
Author:
gbell
Comment:

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  • SOPs/SAMBAMqc

    v14 v15  
    174174A BaRC script (/nfs/BaRC_Public/BaRC_code/R/dupRadar/dupRadar.R) does both the duplicate marking and the analysis with a command like
    175175{{{
    176 # Usage: ./dupRadar.sh <file.bam> <genes.gtf> <stranded=[no|yes|reverse]> paired=[yes|no] outdir=./ threads=1
     176# Usage: ./dupRadar.R <file.bam> <genes.gtf> <stranded=[no|yes|reverse]> paired=[yes|no] outdir=./ threads=1
    177177bsub /nfs/BaRC_Public/BaRC_code/R/dupRadar/dupRadar.R WT.bam /nfs/genomes/mouse_mm10_dec_11_no_random/gtf/Mus_musculus.GRCm38.81.canonical.gtf stranded=no paired=yes outdir=dupRadar_out threads=1
    178178}}}