RNA pipeline reference availability

Q&A
1

I am trying to run the DepMap Omics RNA pipeline on my own data. The pipeline is available here but the genome reference files in the ‘ccleparams’ bucket are not accessible; specifically I’m getting a 403 Forbidden error which I presume means that access to the ‘ccleparams’ bucket is not public (I am using a billing account that is able to download from the ‘cclebams’ bucket).

Is it possible for the genome reference files to be made available? The files I require are:

gs://ccleparams/rna/gencode.v38_with_viral_corrected.gtf
gs://ccleparams/STAR_index_hg38_with_viral.tar.gz
gs://ccleparams/rna/Homo_sapiens_assembly38_with_viral.fa

As a sidenote, I’ve tried to access the reference files for other pipelines mentioned in other posts here but it appears these are non-accessible as well. e.g. Reference WGS data of the cell line fusion gene .

2

Hi, we’ve recently made some updates to how we’re sharing Omics pipeline code and reference files.

The WDL pipelines, which are available in the depmap-omics-pipelines-public Github repo and on Dockstore (e.g. process_sr_rna) now reference files in a public GCS bucket whenever possible.

In your case, all of the files in process_sr_rna’s inputs JSON file are available in the depmap-omics-public-ref bucket.

Note that this bucket is set as requester-pays, so you’ll need to supply a billing project ID in order to download files from it.

3

Thank you. I’ve now managed to download the genome references I needed.