Filtering nuclear RNA expression instead of MT expression in Scanpy
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5 months ago
wonge29 • 0

I was wondering if anyone knows if there is a straightforward way to filter for nRNA expression. I know Scanpy is able to filter mitochondrial reads by first identifying using ["MT"]. Is there a way to do so for nuclear RNA? Or would I need to download anything.. I want to retain MT for certain reasons rather than filtering out high expressions of MT.

filtering nRNA scanpy scRNAseq mtRNA • 311 views
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You asked this question under 3 hours ago on Bioinfo SE. Any reason you're cross-posting it here so soon? Cross-posting tends to annoy both communities involved.

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4 months ago
ATpoint 55k

The MT (prefix) method is actually suboptimal as it will fail once you are not using the trivial gene names but something like Ensembl gene IDs (ENSMUSG...). I personally prefer to load the GTF reference file and then scan for genes that sit on the mitochondrial chromosome (or any other kind of gene type I want to filter for).

As for your problem: What exactly do you mean by nRNA? Is it non-mitochondrial RNAs, or small nuclear RNAs? Please elaborate. If it is anything but the mitochondrial RNA then load a GTF file and select all genes not located on chrM.

Does that make sense?