I am analyzing a 150x2 MiSeq data where there are multiple amplicons from a gene but nested within each other. I want to remove the PCR primers so that I may not get false calls from within primer regions.
I have tried Cutadapt but I am loosing too many sequences due to the nested amplicons.
A primer seq. for one amplicon sits in the middle of another. See image.
What should be the way out? Any help is much appreciated.
Thanks Pierre. I am testing the tool and would update how far I could go.
if the amplified regions without the primers don't overlap, then you shouldn't have any problem.
That is the trouble. They overlap even *after* removing primer regions.
again, you can create two bed files of non-overlapping regions and extract two bams.