How to extract read-pairs that aligned multiple times?
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
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samflag 256?
Tom_L's answer from How to filter/view reads mapped to multiple locations using samtools or pysam
Hi. You can filter out multiple aligned reads using XS:i tags in SAM file.