I have a list of barcodes each 8nt long. I want to look for these barcodes in specific bases (11-18, 47-54, 89-96) of the read 2 sequences allowing 1 mismatch in each region and then filtering the reads that have these barcodes and then match them with the read 1.
I tried at multiple programs like cutadapt, barcode_splitter but they can't be able to handle the method? How can this be achieved?
Thanks for any help you can offer.