Reproducing CERES pipeline using complete cell line data

Q&A
1

Hello,

I tried running the CERES pipeline provided on the DEPMAP portal using the example datasets provided (GECKO - 128 cell lines and WANG - 14 cell lines). I am now trying to run this pipeline on all the cell lines available on DEPMAP (~500 cell lines). However, using the same CERES pipeline, I would need the input files for these complete cell lines (the .gct file and the replicate map). Could you please direct me to the place where I can access to these?

Thanks,
Manasa Lanka

2

Hi Manasa,

You should see about 1000 cell lines in DepMap CRISPR. We do not provide intermediate files to pass into CERES, but you can access the log fold change scores and replicate maps from the Downloads page and reformat them.

Best,
Josh