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I am trying to identify genes that are overall considered to be "actively transcribed" in my cell line of interest for some downstream analysis.

What would the approach be for defining this subset of active genes from an RNA-seq experiments? Any genes with > 1 mapped fragment? Is there a minimum fpkm you would use? or are there some statistics that I can use to identify with some degree of certainty genes that are mostly active in my cell line?

FYI, I am not doing a comparative experiment to identify DEGs, just trying to get a baseline of a group of genes that I can safely considered to be "active" in my cell line.

ricardo3889
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  • Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. – Community Mar 24 '23 at 00:23
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    what do you mean by active? To check if a gene is expressed you can look at the counts. The number of counts depends on the biology. Some genes are only lowly expressed because they are toxic at high levels but essential in the cell/tissue. So without more information it is hard to say how to set thresholds. I assume this is bulk RNASeq, did you sequence 1 sample, do you have replicates, biological replicates/technical replicates etc. – Macintosh Mar 24 '23 at 10:03
  • Well, that is what I am trying to get at with how people are defining "active" genes from a bulk RNA-seq experiment. How would you go about setting a threshold to define a set of MOSTLY active genes in a cell line? – ricardo3889 Mar 24 '23 at 16:56

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