Cutadapt with barcodes in reverse read

Hi @M.Amine.Hassan - thanks for clarifying. In the future, please avoid relying on unreferenced information in another post - we typically answer dozens of user support questions on the forum on any given day, and we often rotate assignment, so it is very unlikely that someone would recognize these two posts as necessarily being related. Feel free to just link to the relate post or posts when you start a new thread! :balloon:

I think you have your order reversed here - it is impossible to demultiplex if you trim your barcodes out of your reads first. As well, q2-cutadapt will return the sequences sans barcodes at this point, so really you only need to demux.

Are that barcodes only in the reverse read? If so, import the forward reads as reverse and the reverse reads as forward. Then, you can use q2-cutadapt to demultiplex (you might need to reverse complement your barcodes).

Be sure to check out the q2-cutadapt Community Tutorial! Keep us posted. Thanks! :t_rex: