Dear team,
I have been downloading single cell fastq files for analysis using software analysis locally such as Cellranger. Is there an alternative way of running my code on fastq files data without downloading it?
Thanks.
Best regards,
Rajesh
Created by rrajesh Thanks! Hello @rrajesh,
The files on Synapse are stored on S3, so the most straightforward way to perform compute will be to download the files. However, we do sometimes allow [STS tokens](https://python-docs.synapse.org/reference/client/?h=sts#synapseclient.Synapse.get_sts_storage_token) to be generated which allows you to interact with S3 objects directly without using the Synapse client. I'm not sure how feasible this will be for reading files into memory and then passing this into a command-line tool like CellRanger, but here is the documentation for this process:
https://help.synapse.org/docs/Compute-Directly-on-Data-in-Synapse-or-S3.2048426057.html
Only certain projects on Synapse support STS tokens as this must be configured before data is added to a project. If you would like to potentially try this, let me know the Synapse ID of the files that you're looking at and I can check if this feature is enabled for those files.
Best,
Will