Felix Krueger

Bismark should just work normally, just point it to the correct folder ``` bismark --genome /my_path/RRBS/ file_trimmed.fq.gz ``` or something similar.

I'm afraid there is isn't supported specifically. As work-arounds you could either make a very small custom genome just containing the region(s) you are interested in, alignments to such small...

I am not sure I can be of great help here as I have never tried to trim PacBio reads before. Trim Galore is specifically meant to be a short-read...

hmm, maybe it does work but it just takes a long time? I would probably first try it out with a small subset to see if it works in principle,...

This is unusual, I would say. Trim Galore has functionality built in that it would die (i.e. terminate) if R1 and R2 input files are truncated, and sequence pairs are...

Hi @AmrSaadeldin , Thanks for the details. Here is my initial assessment of the situation: - in its default mode, Trim Galore looks for adapter contamination, which has obviously worked...

My gut feeling is that you should be fine to proceed as-is, but for your own ease of mind I would potentially run a test (maybe just on a single...

If you still have files called `*trimmed.fq.gz` around in paired-end mode, it is likely that the run hasn't completely finished. Once the validation process is complete, both intermediate trimmed.fq.gz files...

You don't necessarily have to use Trim Galore, but yes some trimming is recommended. the nf-core/methylseq pipeline has an EM-seq switch which should work equally: [--EM-seq](https://nf-co.re/methylseq/2.3.0/parameters#em_seq)

There is quite a lot going on in this list, not quite sure I can give you a good recommendation. I have a few comments: - the TruSeq kit should...