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ayshwaryas / ddqc

Biology-centered data-driven quality control for scRNA-seq
BSD 3-Clause "New" or "Revised" License
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Problematic `ribo_prefix` default setting #4

Open hl-xue opened 1 year ago

hl-xue commented 1 year ago

Hello,

I encountered a problematic behaviour when running ddqc: the estimated ribosomal gene expression percentages are always very low and very different from scanpy estimation. I found it could be related to a bug on the default setting ribo_prefix: str = "^RP[SL][[:digit:]]|^RPLP[[:digit:]]|^RPSA" in ddqc_metrics function. With this string, only RPSA gene was selected in my result, I managed to select all ribosomal genes by setting ribo_prefix="^RP[SL]|^RPLP|^RPSA".

ayshwaryas commented 1 year ago

Thank you, @hl-xue. Feel free to also submit a PR to contribute.