Extract specific reads from mapping of genomes from multiple genomes

Question

[elfeusilva]

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.

[Sukhi Singh]

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?

Answer 1

[Pierre Lindenbaum]

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