Is it possible to work with q2-cutadapt (or any other way) if the barcode sequences are in the reverse reads (Pair-end reads)?
Thanks
Hi @M.Amine.Hassan! What are you trying to do with q2-cutadapt? That plugin currently supports two types of actions: trimming adapter sequence, and demultiplexing multiplexed data. Let us know what you are trying to do and then we can go from there - thanks! 
Hi,
The barcode sequeces are in the reverse reads, usually it is specified in the script to refer to reverse complement of those included in the sample metadata file. Thank you for the support
Hi @M.Amine.Hassan, I still need some guidance from you about what you are trying to actually accomplish in order to help you.
Are you trying to trim reads, or are you trying to demultiplex your multiplexed reads? Or, are you trying to do something not listed here? Let us know! 
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).
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! 
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!
Yes, the barcode sequences are only in the reverse. Thank you for the support.
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