I have r1 and r2 fastq files, a WT reference sequence and a variant reference sequence. I want to find the %WT reads that are chimers. From my understanding, I would need to looking into r1/r2 files and see if half of WT sequence is shared with parts of a variant sequence.
Is there a tool that does this, giving the two reference file (WT and variant sequence) and r1/r2 reads?
PS: I found usearch and also BWA has a chimera flag. When I tried both I got dramatically different results. BWA only found 1 chimera while usearch listed 5. Also, the on chimera found in common was made up of different parts. They both shared the same right piece but the left part was different. I think this could be because the reference sequences are fairly similar. Is this expected behavior? Since they are different how do I determine which one to use?
Any suggestions is appreciated.