Trimming before Stacks

Hi everyone :slight_smile:

I have a list of paired-end files from Rad-Seq sequencing, for which the barcode (which were at the start of the sequences) were removed after demultiplexing. I was wondering though, I now intend to use the stacks series for a denovo map, but I noticed that my sequences all start with a part of the restriction site used (eg in my forward sequences it starts with TGCAG, and in reverse with CGG). Should I trim (with trimmomatic by example) my data before proceeding with the Stacks series ?

Thank you in advance! :slight_smile:

Hi Joelle :wink: ,

If I am not saying a mistake, you donโ€™t have to trim your data between process_radtags step and others Stacks tools.



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Perfect! Thank you for your reply :slight_smile:

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