How to extract read-pairs that aligned multiple times?

Question

[fanicesiza]

Dear all,

I am performing Bowtie2 to align paired-end reads to human genome. Is there any way to get reads that aligned multiple times? Thank you!!

I would really appreciate your suggestions.

Best regards, Jalen

[cpad0112]

samflag 256?

[Bastien Hervé]

Tom_L's answer from How to filter/view reads mapped to multiple locations using samtools or pysam

[Ankit]

Hi. You can filter out multiple aligned reads using XS:i tags in SAM file.