Changes between Version 3 and Version 4 of SOPs/SAMBAMqc


Ignore:
Timestamp:
04/27/16 13:35:15 (9 years ago)
Author:
gbell
Comment:

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  • SOPs/SAMBAMqc

    v3 v4  
    1 = SAM/BAM quality control =
     1= SAM/BAM quality control: Analyzing short read quality (after mapping) =
    22
    33\\
    44
    5 = Analyzing short read quality (after mapping) =
    65
    76== Remove Duplicates ==
    … …  
    5049
    5150
    52 == Quality control after mapping==
    5351== QC to get a (visual) summary of mapping statistics.  For eg. coverage/distribution of mapped reads across the genome or transcriptome ==
    5452
    … …  
    148146}}}
    149147
     148== Graphically representing read duplication ==
    150149
     150The R/Bioconductor package [https://www.bioconductor.org/packages/release/bioc/html/dupRadar.html | dupRadar] can do this, analyzing a BAM file that has had duplicates flagged (such as with Picard's MarkDuplicates tool).
    151151
     152A set of commands can be run with an R script by the package authors available from their [https://www.bioconductor.org/packages/release/bioc/vignettes/dupRadar/inst/doc/dupRadar.html#including-dupradar-into-pipelines | Using the dupRadar package] page.
     153
     154A BaRC script (/nfs/BaRC_Public/BaRC_code/R/dupRadar/dupRadar.R) does both the duplicate marking and the analysis with a command like
     155{{{
     156# Usage: ./dupRadar.sh <file.bam> <genes.gtf> <stranded=[no|yes|reverse]> paired=[yes|no] outdir=./ threads=1
     157bsub /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
     158}}}
    152159
    153160== Interpreting quality control issues ==