Question: Samtools flagstat unpaired reads
0
gravatar for rbronste
2.7 years ago by
rbronste340
rbronste340 wrote:

Trying to quickly remove reads samtools flagstat deems as unpaired from BAM file? Thanks.

samtools bam bowtie2 • 1.0k views
ADD COMMENTlink modified 2.7 years ago by Pierre Lindenbaum127k • written 2.7 years ago by rbronste340

Have you searched Biostars (use external google search) for past threads? There has to be something available already.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by genomax80k
1
gravatar for Pierre Lindenbaum
2.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

remove unpaired files = reads that are not part of a paired-end experiment ?

samtools view -f 1 -b -o out.bam in.bam
ADD COMMENTlink written 2.7 years ago by Pierre Lindenbaum127k

Yes just for BAM files already processed for removal of duplicates (Picard) and ChrM and ChrUN reads.

ADD REPLYlink written 2.7 years ago by rbronste340
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