Difference between gene effects/dependency files

Q&A
1

Hello!
On my way to download the 21Q2 datasets, I saw that there are several versions of the gene effects and dependency files.

First, there are the Achilles/CRISPR difference: as far as I understand the readme, Achilles_gene_dependency.csv use only data from Broad Institute whereas CRISPR_gene_dependency.csv combines these data with data from Sanger Institute.

Second, there is a difference in the gene fitness inference method used. Achilles_gene_dependency.csv uses CERES, the old preprocessor, whereas Achilles_gene_dependency_Chronos.csv uses Chronos, the new one.

So, if I want only data from Broad Institute DepMap and the newest pipeline, I should use Achilles_gene_[dependency|effect]_Chronos.csv, right?
And as Chronos provides significant improvements, will CERES-analysed datasets continue to be provided?

2

Hello!

You are correct that there are Achilles (Broad) and CRIPSR (Broad+Sanger) datasets for both CERES and Chronos in the 21Q2 release, and that the Achilles_gene_dependency/effect_Chronos file is the Broad DepMap data from the newest pipeline this quarter.

We will no longer run CERES, so in future releases all Achilles files will be processed by Chronos. The naming convention for these files will change as Chronos becomes the default, for example Achilles_gene_dependency_Chronos will be named Achilles_gene_dependency in 21Q3.

1 Like
3

Thanks for your precisions!