I have a sample of PE reads that I want to demultiplex. For this I used fastq-multx.
So for instance, my barcode is
And my Forward raw reads :
After fastq-multx, this read has been correctly assigned and trimmed:
However, my Reverse read can be different.. Either I saw:
- No barcode in the reverse read
- Barcode (reverse complemented) in the 5' part:
- Barcode (reverse complemented) within the R reads:
I'm not sure what I have to do with. Should I keep only the PE reads with the one that don't have barcode in the reverse reads ?