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How to remove pseudo genes from a list

I am doing DGE analysis and some of the DEGs that I get seem to be pseudogenes. I was wondering if there is a source or any way to remove the pseudo genes and nonconding RNAs from the count matrix all at once? enter image description here

expression gene differential names
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written by Meghan.T • Meghan.T

1 answer

Use ensembl (either through biomaRt or by downloading the gtf), and use the gene_biotype field to identify the genes you want to keep or exclude.

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written by LChart LChart

Great! Thank you very much!

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written by Meghan.T • Meghan.T

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