I have a question about DMR calling with three cell lines (groups), each with 4–5 replicates. In the documentation, I saw the options

--dmr_population_scale

and

--population_dmrer

, but I’m unsure whether these are meant for much larger “population-scale” experiments and if they are appropriate for my setup. I’d also like to compare DMRs in one cell line against all others. Is there a way to do this within a single run, or do I need to specify

--dmr_a

and

--dmr_b

for each pair (e.g. three separate runs to cover all combinations)? In other words, can the pipeline perform all pairwise comparisons between 3 groups in one go, or must they be run separately? And what options would I have to set for that in my script? Any guidance on recommended settings for this design would be greatly appreciated.

I think you might be in the wrong channel, if you are referring to a specific pipeline please go to the relevant channel 🙂

Hi, @Magdalena Winklhofer! Slack uses channels to organise discussions. Press the

...

more option on the left sidebar. Then hover over Your organisation, and finally select Channels to browse. Each nf-core pipeline has it’s own channel (e.g. #CE8SSJV3N). Please post any questions about specific pipelines in the relevant channel. If you’re not sure where to post your message, please ask @James Fellows Yates for help.

I posted my question now in the methylong channel, but still did not get any reply. Could you let me know if I am still in the wrong channel?

Hrm, you can try pinging the main developer of the pipeline