About the genome and gene version in "DepMap Public 21Q3" CCLE_expression.csv file

Q&A
1

Hi all,
When I look at the TOPMed_RNAseq_pipeline, GRCh38 reference genome and GENCODE 34 annotation is used, but it seems the genes of 21Q3 RNAseq data is not concordant with GENCODE 34 gene set.

We have RNAseq data of several cell lines, and we want to process these data using the same databse and pipeline as in CCLEdatabase. So can you tell me which genome and gene version was used in the 21Q3 CCLE gene expression data.

Thanks you!

2

Hi, a similar question has been posted here. Please let me know if the information there answers your question. -thanks