Running into a weird problem I’m helping to trouble shoot. We have a run which may have some technical issues, which we are re-running, but wanted to see if we could use only the forward reads to de-multiplex and annotate.
Essentially, the forward and reverse runs are in fastq files and the barcode is in another fastq files. I realized that since the barcode is not in the sequence itself it is not useful if I use cutadapt. The forward read/reverse read fastq/barcode fastq have been performed through the EMP protocol. Illumina MiSeq.
Here’s what I already looked at:
Thanks for any input.