CRISPR knockout screen sgRNA enrichment file

Q&A
1

Dear DepMap Community

I am interested in CRISPR knockout screen sgRNA enrichment file to identify genes inducing cancer cell proliferation. There are many files on the DepMap portal. It would be helpful if some one can advise which one is the sgRNA enrichment file.

Thank you

2

There is no sgRNA enrichment file per se, but positive scores in the logfold change files indicate enrichment.

3

Thank you Joshua!

Are the logfold changes in the file normalized to reference or controls? OR Is there a way I can normalize?

Thank you again!

4

Log fold change values are normalized to the initial pDNA abundance.

5

Thank you Joshua!

I am analysing DepMap Public 21Q2 Achilles_logfold_change.csv 05/21 data on the portal. Where I can locate the normalization file for this data?

Thank you

6

I’m not quite sure what that would be, but the entire pipeline and each intermediate file is described in the README, which also includes some references with more details.

7

OK thank you. Appreciate your guidance