Question: Bowtie2 alignment: Reads that aligned concordantly >1 times
0
gravatar for elfeusilva
4.9 years ago by
elfeusilva0
Afghanistan
elfeusilva0 wrote:

Hello Guys!

I would like to extract reads that "concordantly >1 times" from SAM output file and make a new file with only this reads [reads that aligned concordantly > 1 times]. I did a alignment on Bowtie2 software.

Thanks very much.

35133445 reads; of these:
  35133445 (100.00%) were paired; of these:
    33688527 (95.89%) aligned concordantly 0 times
    1373944 (3.91%) aligned concordantly exactly 1 time
    70974 (0.20%) aligned concordantly >1 times [make a new file with this reads.]

 

score bowtie map alignment bowtie2 • 3.7k views
ADD COMMENTlink modified 23 months ago by Biostar ♦♦ 20 • written 4.9 years ago by elfeusilva0
3
gravatar for Devon Ryan
4.9 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

Something like samtools view -h foo.bam | grep -v "NH:i:1" | samtools view -Sbo foo.multimappers.bam - will probably work. You could also just pipe to a SAM file rather than samtools if you want.

ADD COMMENTlink written 4.9 years ago by Devon Ryan91k
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