I am trying to analyze CutnRun data. It recommends suing Kseq tool for trimming (to trim up to 6-bp adapters from the 3′end) and Dovetail alignment in Bowtie2. Does anyone have any experience in setting this up in shell command script.
I am now doing the same - did you get an answer to your question?
Hello! I am on the same path here...did you get any answers? I am mostly concerned about the Kseq commands. Thank you!
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