Finding a specific reference file for GTEx

1

Hi,

I’m trying to replicate the GTEx RNA-Seq pipeline (gtex-pipeline/rnaseq at master · broadinstitute/gtex-pipeline · GitHub).

It requires an RSEM reference file that I cannot find in the GTEx workspace, or Gen3.
It’s hosted in this Google bucket (Google Cloud Platform) but I’m having trouble downloading from there. So was hoping to find a solution on Terra.

Edmundo

2

Hello,

Thanks for writing in about this and we can definitely help you locate this file. What sort of trouble are you having when trying to download the file from the Google bucket?

Kind regards,
Pamela

3

Hi,

I’m reformulating my question.
The reason I need the specific reference file is to replicate the GTEx RNA-Seq pipeline (gtex-pipeline/rnaseq at master · broadinstitute/gtex-pipeline · GitHub) I mentioned before.

Can this docker implementation be done directly on the data hosted in AnVIL/Terra?

Best,
Edmundo

4

Hi Edmundo,

Is the file that you need for the pipeline already in Terra? If it is not, you should be able to run the docker implementation in Terra and pull the necessary file into your Terra workspace using gsutil. You can find more information about transferring data to/from Terra in this article: https://support.terra.bio/hc/en-us/articles/4409101169051-Moving-data-to-from-a-Google-bucket-workspace-or-external-

Please let me know if this is helpful and if you have any additional questions. I’m not quite sure what you are asking for but I am happy to help in any way I can!

Kind regards,
Pamela

5

Hi Pamela,

Thanks for the information!
I did find a similar implementation in the Workflows section.

I do still need to pull the file to my workspace, however I need to specify a “Project Identifier” in gsutil.
Where do I find this?

Edmundo

6

Hi Edmundo,

Are you referring to the “project to bill” when downloading the file from the Google bucket? This would be the project ID of your workspace Google project, which can be found on the right-hand side of your Terra workspace. You can find more information about this here: https://support.terra.bio/hc/en-us/articles/360029801491-Using-Requester-Pays-workspaces-buckets#:~:text=Requester%20Pays%20is%20an%20optional,data%20from%20a%20different%20region.

Is this what you are looking for?

Kind regards,
Pamela