Question: Bowtie2 alignment: Reads that aligned concordantly >1 times
gravatar for elfeusilva
4.9 years ago by
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
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
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 835 users visited in the last hour