Do we need to filter out the 0 counts sgRNA in CRISPR analysis?

Hi,

I’m doing CRISPR analysis and there is a question, when we perform CRISPR analysis, is there a step to remove low count sgRNAs from control and/or treatment samples?

The reason of this question is that, if sgRNA(A) has a very low control count (perhaps 0) and a moderate treatment count (perhaps 500), it will have a higher logFC than sgRNA(B) which has a moderate control count (perhaps 500) and a high treatment count (perhaps 10000). However, biologically speaking, sgRNA(B) should be more interesting, as the treatment count is very high and it takes up a bigger portion of the treatment (sorted) sample sgRNA pool.

Is there any suggestion on this problem?

Thanks!
Leran