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python-3.xrna-seqscanpy

How to get specific RNA sequence of Anndata?

I have a question where I don´t know how to start this. We did a scRNA sequencing experiment and I now have an AnnData dataset. I already know a lot about this dataset mainly by using scanpy library and I would like to "finalise" the analysis by extracting genes that have a specific RNA sequence in the 3'UTR. Unfortunately I have no idea how to approach this since I am no bioinformatician and couldn´t find a tutorial to do this. Can someone please help me with this problem?

Here how it looks like. enter image description here

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Thanks in advance!

Solution

  • I just found a way around in R. It is on the bases on BSgenome.Mmusculus.UCSC.mm10. You can find the answer here. Just read in the result in python as a list and us the function sc.tl.score_genes to see where they are enriched.