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Filtering nuclear RNA expression instead of MT expression in Scanpy

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
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updated by mt_pereira • mt_pereira • written by wonge29 • wonge29

1 answer

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?

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written by ATpoint ATpoint

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