Design file example confusing

[MareikeJaniak]

Hi!

I was helping a student with a chipseq issue today and I realized that there is something confusing in the documentation. On the genpipes tutorial page, the section about creating a design file (https://genpipes.readthedocs.io/en/latest/tutorials/genpipes_tutorial.html#creating-a-design-file) uses a chipseq design file as an example, even though chipseq design files are different from the other design files. I also think it's using an outdated chipseq design file format. (It's correct on the actual chipseq pipeline page: https://genpipes.readthedocs.io/en/latest/user_guide/pipelines/gp_chipseq.html).

Correct me if I'm wrong, but maybe it would be better to replace this example (https://genpipes.readthedocs.io/en/latest/tutorials/genpipes_tutorial.html#creating-a-design-file and the following section) with an rnaseq example or something similar that's more representative of a standard design file? @pphector, what do you think?

[shaloo]

@MareikeJaniak thank you for pointing this out! 👍

I have updated chips. Will discuss with @pphector this Tuesday and if he recommends, will open a new GitHub issue and update the tutorial example to RNASeq. Can u pls share some design file / example content with me? We can set up a call this week if appropriate and I can gather all inputs from you to update the present chipseq design tutorial section to RNAseq one. okay?

[MareikeJaniak]

Attaching the example design file for rnaseq here. I think we can just use the example data for rnaseq, right? Happy to have a call to help. design.rnaseq.txt

[MareikeJaniak]

Looks like I already sent this! Let me know if this is enough to put together the example and replace the current chipseq example. If not, I can try to write up a draft of something.

[shaloo]

@MareikeJaniak @pphector Regarding the design file shared above for chipseq tutorial example here: https://genpipes.readthedocs.io/en/shaloo-gp-5.0-layout/tutorials/genpipes_tutorial.html#chipseq-test-dataset

Is it the same for both protocols? chipseq and atacseq? Lmk and I will update it for 5.0 docs. I'm assuming we need to update 4.6.1 docs as well or not?

[MareikeJaniak]

The current description looks correct to me.

[shaloo]

Closing it. Thx.

[shaloo]

JFYI Updates for 4.6.1 are done here but not published through the RTD version flyer (dropdown)as discussed in July / last call.