Choosing the correct pDNA

Q&A
1

Dear DepMap-Team,

I am relatively new to CRISPR Screen data science and would like to compare your data to the JACKS and MAGeCK data of our lab. For this purpose, I intend to use your raw read counts as JACKS/MAGeCK input.

I was wondering about the meaning of p in the replicate name, also about which pDNA to use as D0-sample. I understand the concept of the different batches. However can I randomly choose any pDNA within each batch as D0-sample or do you recommend a different approach i.e. aggregation.

Thank you very much,

Alex

2

Hi Alex,

I recommend against trying to interpret the replicate IDs. There is no consistency to their formatting and they will lead you astray. Treat them as random strings. Each release comes with an Achilles_replicate_map file that connects replicate IDs to cell lines and pDNA batches. In terms of pDNA batch aggregation, we sum all pDNA belonging to the relevant batch and then normalize. This will be a bit less noisy than using an individual measurement.

3

Dear Joshua,

thank you very much for the fast reply and the information.

Best,

Alex