New CUT&RUN tutorial with Workflow for Training and Workflow for a bigger data analysis

[heylf]

Dear @shiltemann @bgruening @lldelisle, I need some revision for the CUT&RUN training material.

• [ ] Test data is ready (two replicates paired-end, down sampled and a ChIP-seq peak file, total 5 files a 30-40 MB). If the training material is ok, then I will upload it to zenodo. Training workflow can be executed within 30 minutes. Sometimes MEME-ChIP can be slow.
• [ ] Please check if something is missing.
• [ ] I wanted to include a secondary motif detection. The perfect tool would be Spamo (included in MEME-ChIP, but it is currently deactivated). Is it possible to activate this easily in the MEME-ChIP tool wrapper?

[heylf]

Forgot to ask is there a snippet to create a dataset collection @hexylena

[shiltemann]

Forgot to ask is there a snippet to create a dataset collection @hexylena

Here are the collection FAQs (snippets) we have available currently: https://training.galaxyproject.org/training-material/faqs/galaxy/#collections

feel free to edit them if you need or add new ones

[lldelisle]

I think you could add somewhere the link to the protocol: https://dx.doi.org/10.17504/protocols.io.zcpf2vn

[heylf]

Thank you @lldelisle for your time :) I have made some changes!

[lldelisle]

You are welcome. Maybe you can add me as 'editing author'. Have you thought about HOMER (findMotifsGenome) for motif detection?

[heylf]

I already added you as editor :).

I have not considered it. You think it outperforms MEME-ChiP?

[lldelisle]

I don't know. In my lab we use it. It is already in usegalaxy.eu.

[heylf]

I don't know. In my lab we use it. It is already in usegalaxy.eu.

Mmm. I have quite good experience with MEME-ChIP. Maybe good to compare the two tools at some point. Thank you lucille for the recommendation.

[lldelisle]

Hi @hexylena and @heylf, If I am not wrong. For the moment these slides are just copy paste from ATAC-seq.

[heylf]

Yeah sorry I had the slide from the ATAC-Seq tutorial in there.

[heylf]

@lldelisle anymore suggestions? Else I would go on an upload the data to zenodo and prepare the tutorial for the final merge.

[lldelisle]

I think you can go for the upload in zenodo and prepare the tutorial. Then, I will run it and recheck carefully. Is it ok for you?

[heylf]

@lldelisle I uploaded the data to zenodo.

[lldelisle]

I accidently pushed my commit directly to your branch instead of writting a PR... Sorry.

I corrected:

• use of collection
• use last version of tools
• replace apply rule by select dataset which seems more natural
• simplify the bed intersect because if you use the option reciprocal you don't need to do 3 intersect as it gives the same result as a single one
• I could not find the number of peaks with the GATA motifs in the MEME-ChIP output.

[lldelisle]

This needs a second review.

[bgruening]

Do you think we can get this as draft in? I might have a user that would like to test it and provide feedback.

[shiltemann]

Sure, anything can go in as draft as far as I'm concerned (as long as the build test passes)

[bgruening]

Not sure why this is failing to build @shiltemann?

[shiltemann]

@bgruening fixed (snippets don't always render well if they don't have empty lines above and below them).

And merged, should show up on our new stellar nursery page soon: https://training.galaxyproject.org/utils/stellar-nursery

[bgruening]

Upps, ok good to know, will try to remember this.

[bgruening]

Thanks!!!