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Introducing description on how to proceed with result files #198

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Introducing description on how to proceed with result files #198

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smoe
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@smoe smoe commented May 25, 2023

Hello,
I had a long stare at the cut'n'run result files and now came up my own little downstream workflow to finally have some gene lists and FASTA files. This patch extends the workflow description accordingly.
I happily extend this description along with what your comments may be suggesting.

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github-actions bot commented May 25, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b313ac3

+| ✅ 155 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '3.2'
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-15 18:13:36

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Hi @smoe, could you just describe to me how this is different to our consensus peak calculation?

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smoe commented Jun 15, 2023

Hi @smoe, could you just describe to me how this is different to our consensus peak calculation?

The meta-context is that I felt very much insecure about how I should approach the data. You have no idea about how valuable your comment is for me to start to believe that I am somewhat close to the right track. To answer your question - my approach allows to fill a Venn diagram when having multiple groups - for us it is multiple isoforms of a transcription factor, so you can filter not only for peaks that are consistent within a group but you get set differences, like the peaks in group1 and group2 but not in group3.

What I would want to propose is to generate that Venn diagram, and I would also want to start MEME on the sequences represented for each subset of the Venn diagram. Also, I think the workflow should list the genes that are associated with the peaks from each subset of the Venn diagram. I would be prepared to provide that in a separate PR, and I happily integrate your consensus peak calculation with the description I have provided. The current description of the workflow does not point to the files that should be expected as consensus peaks and in my run I did not find them - maybe because the group size of ours is just 1?

If you could direct me a bit about what you liked about my write-up and what you would like to read differently, then I would happily address that. Maybe you could also add a section "to be implemented" in the documentation so I would know what to address/implement?

@smoe smoe mentioned this pull request Jul 20, 2023
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@smoe smoe marked this pull request as draft November 14, 2023 21:31
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@smoe @chris-cheshire