I want to know how to identify and remove pseudogenes from BRCA samples? I have read lots of paper but didnt find relevant information. Please let me know about it. Thanks in advance.
Pseudogene is an annotated gene type in the reference GTF file, e.g. from GENCODE. You can parse the gene names from there and then remove it from e.g. your count matrix. For more advise you'd need to add details on what you tried and from what format you want to remove the genes.
Thank you for the information.
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