Non mapping sequences in genome
1
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.
RNA-Seq
• 408 views
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.
Login before adding your answer.