hello...I'm new to Ribo-seq method and this riboseq pipeline. I'm reading some papers where they say that they trim poly A tails and remove specific adapters. For instance in this SARS2 paper, they say "linker (CTGTAGGCACCATCAAT) and poly-A sequences were removed". How do I set the right parameters to the pipeline so that these sequences are removed? CTGTAGGCACCATCAAT is not a sequence identified by TrimGalore. Also, I don't think multiple adapter sequences can be set for TrimGalore to search for. I've never used fastp so not sure if that is an option.

Those are the only trimming options in place right now. I would probably experiment with the options from the documentation of those tools to see if you can make them do what you need, and then look at passing those options on the workflow.

Perhaps the adapter's were already trimmed when the data was uploaded? Might explain why trimgalore didn't find them?

This is from `trim_galore --help`:

multiple adapters can also be specified like so:
                        -a  " AGCTCCCG -a TTTCATTATAT -a TTTATTCGGATTTAT"
                        -a2 " AGCTAGCG -a TCTCTTATAT -a TTTCGGATTTAT", or so:
                        -a "file:../multiple_adapters.fa"
                        -a2 "file:../different_adapters.fa"
                        Potentially in conjucntion with the parameter "-n 3" to trim all adapters. Please note
                        that this is NOT needed for standard trimming!
                        More Information here: <https://github.com/FelixKrueger/TrimGalore/issues/86>

Thank you everybody! Also I found that fastp has the

--adapter_fasta

option to give a FASTA file with multiple adapters.