get rid of redundant reads in BOWTIE2

Question

[andynkili]

Is it possible to get every reads that match several loci on the reference (using the read mappers bowtie2)?

I've looked for any options allowing to do so, but I'm only aware of the --al option, saving all the reads that matched the reference sequence. The ultimate goal is to keep only the reads that have a unique position (match) in the reference sequence, i.e the reads that can be trusted regarding their position.

Answer 1

[GouthamAtla]

How to extract unique mapped results from Bowtie2 bam results?

Best Way To Get Truly Unique Reads In Bowtie/Sam?

Bowtie2, -M Alignment/Reporting Mode

[andynkili]

THANK YOU !