# RNA pipeline reference availability 

**URL:** <https://forum.depmap.org/t/rna-pipeline-reference-availability/4646>\
**Category:** Q&A\
**Created:** [June 25, 2026, 8:46pm UTC](https://forum.depmap.org/t/rna-pipeline-reference-availability/4646 "2026-06-25T20:46:55Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![tlee](https://avatars.discourse-cdn.com/v4/letter/t/258eb7/32.png) [@tlee](https://forum.depmap.org/u/tlee)\
**Post date:** [June 25, 2026, 8:46pm UTC](https://forum.depmap.org/t/rna-pipeline-reference-availability/4646/1 "2026-06-25T20:46:55Z")

</div>

I am trying to run the DepMap Omics RNA pipeline on my own data. The pipeline is available [here](https://github.com/broadinstitute/depmap-omics-rna) 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](https://forum.depmap.org/t/reference-wgs-data-of-the-cell-line-fusion-gene/2694) .

---

<div class="post-metadata">

**Author:** ![Devin\_McCabe](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/devin_mccabe/32/1642_2.png) [@Devin\_McCabe](https://forum.depmap.org/u/Devin_McCabe)\
**Post date:** [October 20, 2026, 6:59pm UTC](https://forum.depmap.org/t/rna-pipeline-reference-availability/4646/2 "2026-10-20T18:59:32Z")

</div>

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](https://github.com/broadinstitute/depmap-omics-pipelines-public) Github repo and on Dockstore (e.g. [process\_sr\_rna](https://dockstore.org/workflows/github.com/broadinstitute/depmap-omics-pipelines-public/process_sr_rna:main?tab=info)) 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](https://dockstore.org/workflows/github.com/broadinstitute/depmap-omics-pipelines-public/process_sr_rna:main?tab=files&file=%2Fwdl%2Frna%2Fprocess_sr_rna%2Fprocess_sr_rna_inputs.json) are available in the `depmap-omics-public-ref` bucket.

Note that this bucket is set as [requester-pays](https://docs.cloud.google.com/storage/docs/using-requester-pays#using), so you’ll need to supply a billing project ID in order to download files from it.

---

<div class="post-metadata">

**Author:** ![tlee](https://avatars.discourse-cdn.com/v4/letter/t/258eb7/32.png) [@tlee](https://forum.depmap.org/u/tlee)\
**Post date:** [October 21, 2026, 7:30am UTC](https://forum.depmap.org/t/rna-pipeline-reference-availability/4646/3 "2026-10-21T07:30:16Z")

</div>

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