Output uncorrected tables without going through all of curate

kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics

BSD 3-Clause "New" or "Revised" License

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Output uncorrected tables without going through all of curate #147

Closed Hego-CCTB closed 7 months ago

Hego-CCTB commented 10 months ago

We recently encountered a case, where samples were (intentionally) extremely similar to each other, despite being tagged as different tissues. This led to amalgkit removing a couple of samples. Additionaly for that dataset, we didn't need the amalgkit corrected output at all. So it would be nice to have an option to just output all data before the SVA correction and then stop, saving some time in cases where SVA correction is not desired.

Hego-CCTB commented 7 months ago

Done here: 9a63d9dfd7cb9e30db31a8d341adceea6bab73c7

--skip_curation yes stops curate after the transformation of the count table and the curate_group.mean version of that table and before any kind of batch-effect removal/outlier removal/mapping-rate cut-off. --skip_curation no behaves normally (default. https://github.com/kfuku52/amalgkit/commit/22e34c6d2779138bb7729d37e300a89fab9b54a9).

kfuku52 commented 7 months ago

Thank you. Could you bump the version?

Hego-CCTB commented 7 months ago

done