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Extract specific reads from mapping of genomes from multiple genomes

Hello Guys,

Did the mapping of multiple genomes in bowtie software. I indexed multiple genomes, and then did the mapping of reads in bowtie. I would like to extract the reads that were mapped in each genome separately. This is possible using the Picard or other tools?

Thank you.

genomes mapping samtools bowtie
• 2,456 views • link
updated by Ram Ram • written by elfeusilva • elfeusilva
The files containing mapped reads should be separate, unless you merged the fasta files of all the genomes you are working on and then indexed it. Anyways, why would you do that?
• 0 views • link
written by Sukhi Singh Sukhi Singh

1 answer

Extract the name of the mapped reads (forward or reverse) using samtools with option -F/-f.

sort | uniq those names

find the reads in each genomes using comm

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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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