I am trying to find CRISPR KO data on the MARCH family of genes (MARCHF1 - 11). I found the related post below about MARCHF5 missing data but it seems like none of the family members have data from CHRONOS. However, it looks like gRNAs for these genes were included in the screen and not removed during analysis according to the AvanaGuideMap.csv file. I am wondering what happened to that data. Thanks,
Gene of interest now missing in Avana screens in 2021 DepMap - Q&A - DepMap Community Forum
This seems like the old issue where excel autocorrects a gene name to a date. I checked Feb1-7 and Sept1,10,11,12,14 they are all missing CRISPR entries as well. Interestingly Feb1-7 has no data associated with it. Can this be fixed? Thanks,
I took a look and the issue is similar to what happened in Gene of interest now missing in Avana screens in 2021 DepMap but the root cause is slightly different.
The CRISPR data that is loaded into the portal at this time is a combined dataset merging data from the Avana library (used by CRISPR screens done at the Broad) and the KY library (used by CRISPR screens done at Sanger), and the method of merging can only retain those genes which are in the intersection of those two libraries.
Previously, we were also loading a 2nd dataset which contained the un-merged version of the Avana screens, and so when you looked up a gene which was not present in the merged dataset, you would see the profile from only the Avana library. (Which is how the issue was resolved in the previous forum post)
However, in this latest release we changed the files that comprise a depmap release, and no longer release a file containing only Avana screening data.
Instead we are releasing a new file named ScreenGeneEffect.csv which contains the Avana screens (and potentially others in the future). The Avana data for this gene should be present in this new file, but this new file isn’t used by the portal.
In the next DepMap release, this problem should go away as we’re planning on changing the methodology used to merge datasets. After that switch, the genes which were only screened by the Avana library will appear in new versions of CRISPRGeneEffect.csv, resulting in the missing genes re-appearing on the portal.
Thanks Phil. Thats helpful.