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Need ability to annotate RNAseq files with additional keys for crispr/drug tx #320

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allaway opened this issue Jul 13, 2023 · 4 comments · Fixed by #502
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Need ability to annotate RNAseq files with additional keys for crispr/drug tx #320

allaway opened this issue Jul 13, 2023 · 4 comments · Fixed by #502
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@allaway
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allaway commented Jul 13, 2023

Describe the issue with the metadata
Currently the RNAseq manifest does not allow me to add genePerturbed, genePerturbationType, genePerturbationMethod, or experimentalCondition, which is helpful when annotating drug treated cells that also have crispr/sirna/shrna modifications. I think we removed these on purpose a while back, but now I miss them. I think we used to have them in the "extended" genomics assay manifest - maybe we should bring that back?

@allaway allaway added the bug Something isn't working label Jul 13, 2023
@anngvu anngvu self-assigned this Jul 24, 2023
@anngvu anngvu moved this to Todo in NF-OSI Sprints Jul 24, 2023
@anngvu anngvu moved this from Todo to In Progress in NF-OSI Sprints Jul 28, 2023
@anngvu anngvu assigned aditya-nath-sage and unassigned anngvu Aug 19, 2024
@aditya-nath-sage
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@allaway @anngvu is this in relation to RNASeqTemplate or ScRNASeqTemplate?

@anngvu anngvu linked a pull request Aug 23, 2024 that will close this issue
@anngvu anngvu closed this as completed Aug 23, 2024
@github-project-automation github-project-automation bot moved this from In Progress to Done in NF-OSI Sprints Aug 23, 2024
@allaway
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allaway commented Sep 5, 2024

@aditya-nath-sage - sorry that I missed this question. I was talking about RNA-seq, but it would make sense to add this to scRNAseq too. What do you think?

@aditya-nath-sage
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I could definitely add it to scRNAseq as well, I'll create another branch and do this.

@allaway
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allaway commented Oct 15, 2024

Also needed to add these columns today in the epigenetics sequencing assay template. might be nice to incldue them there too!

@anngvu anngvu closed this as completed Oct 31, 2024
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3 participants