Hello @thermokarst
Thank you for the support
As indicated in one of my previous post, I have only forward and reverse reads without barcode.fastq file.
I am trying to trim the reads from the barcodes and demuxltiplex. This issue is in a way redundant of this post.
The samples were barcoded in the reverse reads, however in cutadapt demux-paired, I could only provide --m-forward-barcodes-file. Does this work although the barcode sequences are in the reverse reads?
Ultimately, it would be very much appreciated if you could provide a test example where the barcode.fastq file is not provided (multiplexed Vs demultiplexed reads , barcode sequences in forward vs reverse reads).