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rna-qc - #36

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Johnnyassaf wants to merge 42 commits into
mainfrom
rna-qc
Open

Johnnyassaf wants to merge 42 commits into
mainfrom
rna-qc

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@Johnnyassaf

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Purpose

-Adding QC steps to rna seq pipeline, opening this pr to test where im at

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  • Related GitHub Issue created
  • Tests covering new change
  • Linting checks pass

@Johnnyassaf

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For RNAQC I have three options for the Picard collect rnaqc metrics:

-Run non-spot with high mem (expensive but reliable)
-subsample reads and run it with spot (fastest 10 min vs 3 hours) and much cheaper (but is it representative?)
-Run spot with high mem (cheaper (0.8 ish vs 1.6) than non-spot per sample for expensive samples)

I reckon subsampling is good enough, but leave this question open to comments

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