how to extract alignment concordantly exact 1 time from bowtie2 output

Question

[Wasim]

Hello, I have aligned WGS with reference seq using bowtie2 but I want to extract those which aligned concordantly exactly 1 time. It will be a great help if any one guides me on how can I extract them.

Best

Answer 1

[GenoMax]

Prior threads that may be of use:

How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Bowtie2 alignment: Reads that aligned concordantly >1 times (remove -v from grep).