Felix Krueger

To just quickly chip in here. It is correct that the option `--polyA` in Trim Galore is designed to work with an RNA kit which specifically produces reads from polyA...

Hi Harshil, yes, `args = '--fastqc -a {A}10'` should work straight out of the box, but again, this will not be on top the adapter (auto-detection) and trimming, but this...

It wouldn't necessarily be the entire pipeline twice, but just add an extra trimming step. So something like the nf-core equivalent of: ```nextflow TRIM_GALORE (file_ch, params.outdir, params.trim_galore_args, params.verbose) if (PolyX_trimming_will_make_my_day){...

but yea, in the end the results will be pretty much the same however you implement it :P

For `--polyA` with the Collibri kit, it was actually a little complicated. But the bottom line was that you need to remove poor qualities and sequencing adapters first, and then...

I think I have now generated a new PR against the updated structure: https://github.com/nf-core/modules/pull/45

So maybe this can be closed?

I agree, it might be a nice pipeline to have. The tools mentioned above were - of course (in good old bioinformatics manner) - shown to be much superior to...

Trim Galore removes poor qualities from the 3' end of sequence, but does not do this from the 5' end (as it is never really needed). If you have some...

Regarding your second question: I haven't looked at the ENCODE-DCC pipeline myself, but you could either - align the data genome-wide and just look at your genes of interest, or...