Proper threshold in RNA-seq RPKM data to determine which genes are expressed in a cell line

Q&A
1

I am currently working with a whole genome CRISPR screen dataset in HELA cells and I need to use DepMap RNA-seq data to filter out genes which are not expressed endogenously in HELA. I was wondering if there is a way to determine a RPKM threshold for genes which are considered not expressed?

Thanks!

2

Thanks for contacting our forum. As far as I know there isn’t a universally accepted answer to this question. So unfortunately we don’t have any specific suggestion on this. A similar question also came up here that I’m linking to for your reference.

-thanks
Javad

3

Thanks Javad, appreciate the feedback.

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