Non mapping sequences in genome
How can I extract the sequences that didn't match with the reference genome? I need those in usable file, not just to eliminate them.
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GenoMax
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written
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Marcela Moncada •
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written
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Marcela Moncada •
1 answer
If you were using bbmap.sh (aligner from BBMap package) then you can collect unmapped sequences using outu= option. Something like
bbmap.sh in1=R1.fq.gz in2=R2.fq.gz outu1=R1_unmap.fq.gz outu2=R2_unmap.fq.gz ....
Some other aligner will also allow you to do this during mapping. Otherwise you can use samtools later to filter these from aligned data files.
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