Trimmomatic Kseq and Bowtie --dovetail

Question

[KT]

Hello,

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.

[blur]

I am now doing the same - did you get an answer to your question?

[drosophila2020]

Hello! I am on the same path here...did you get any answers? I am mostly concerned about the Kseq commands. Thank you!