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Add automated quality control checks before submitting data to Gemma #51

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arteymix opened this issue Jan 15, 2021 · 0 comments
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@arteymix
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As per https://github.com/PavlidisLab/GemmaCuration/issues/3#issuecomment-759691608, it would be valuable to perform some sanity checks before submitting data to Gemma.

Here's a list of basic things that we can do:

  • detect samples with zeroed-out expression vectors (this could be caused by an alignment failure, or too short reads, etc.)
  • ensure that every column have enough variance
  • add a Luigi parameter to manually skip QC checks
  • report QC checks in the Web viewer
  • report QC checks on Slack (in case of failure)
@arteymix arteymix self-assigned this Jan 15, 2021
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