Multiplexed FRP on cellranger_multi

[Andrew Navia]

Hi Cumulus,

I'm trying to align some 10X flex data with cellranger_mulit following this protocol. The input options are quite different from what's written in the doc however and don't include the described sample sheet. 

When I run the pipeline with what I think are the corresponding inputs, the error I'm getting is related to pulling down the fastq paths (CommandException: No URLs matched: gs://fc-secure-d0f3c438-af32-4054-8437-db0a36aff42c/30May24/FASTQs/CHCA_AWN1/CHCA_AWN1/CHCA_AWN1). The path is copied directly from my bucket. Any help with this/which parts of the described samplesheet should be input where would be appreciated.

Thanks,

Andrew

[Yiming Yang]

Hi Andrew,

It looks like this GitHub issue is yours: https://github.com/lilab-bcb/cumulus/issues/406. But it was about a different issue other than in your email.

Just to follow up, can I assume that the path not found issue has been resolved in your case? And for the chemistry issue, could you please let me know which FRP setting was used in your data? You may see the details by reading through my response to that GitHub issue.

Sincerely,

Yiming

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