do files specified in this issue exist already? needed for GO-MWU (enrichment tool)

[grace-ac]

Do either of the files listed below in bold exist somewhere already?

I tried GO-MWU earlier, and I used the list of DEGs from the 2019 crab data to perform analyses. Results = no enrichment.

GO-MWU is meant to be used with the full list of inputs, meaning that I should have used all 2019 crab dataset. (GO-MWU README.md if you want more info)
Now that I've figured out how to use GO-MWU, I'd like to try again with the correct data.

I need to make 2 files for GO-MWU, but in order to make them, I need:

1. blast output of JUST the 2019 crab data, which I will join with the 2019 gene count table. Then I'll create the first file needed: two columns --> geneID, and GO terms
2. full list of 2019 crab genes (not just DEGs) from DESeq or edgeR. Then I'll make the second file: 2 column file: gene ID and a column of measures of significance associated with GO enrichment (examples: kME value, p-value, dN/dS value, etc) - i'd like to use p-value.

Let me know if anything above is unclear.

[sr320]

I would say you need to use transcriptome ref assembly annotation for this but lets discuss.  Also I think DAVID is certainly worth a whirl.

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On Apr 20, 2020, 3:52 PM -0700, grace-ac ***@***.***>, wrote: Assigned #908 to @sr320. — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or unsubscribe.

[kubu4]

The short answer to both questions: no.