Specific gene model used in 22Q1 CCLE RNASEQ files

Q&A
1

Hi,
I’m trying to replicate the results of the CCLE 22Q1 results by using the published GTEX/TopMed RNASEQ pipeline. Which gene model is used for this release? I see GENCODE v34 mentioned in the github md file, but GENCODE v26 is mentioned in the Docker release for V8. Is GENCODE v34 the one being used in the most recent release?
Thank you!
Best,
Revonda

2

Hello rmehovic,

Sorry for the delay! You should be able to find every info about this in our github project, at the corresponding commit (named 22Q1 for 22Q1, etc…)

I believe in 22Q1 we used gencode v33 for fusions depmap_omics/all_configs.json at 22Q1 · broadinstitute/depmap_omics · GitHub
and gencode v29 for expression
depmap_omics/all_configs.json at 22Q1 · broadinstitute/depmap_omics · GitHub

Hope this helps,
Best,