I have a list of contaminants that I want to filter out from my paired end:
bowtie2 -x contaminants -1 pair1.fastq -2 pair2.fastq -S out.sam
Now I want to extract only unmapped reads from the .sam file but I want to keep only paired end.
So if read1 map somewhere and read2 not, I want to discard these PE.
1) How can I do that ?
2) Is it possible to produce 2 sams file at the end (one for each PE) ?