Does cumulus support cellranger multiomics between gene expression and vdj?

[Wesley Kwong]

Hi,

 

I’m having trouble trying to process an example dataset from 10X, which contains both gene expression and vdj data, using the cellranger multi command from the cumulus workflow (ver 2.2.0) on Terra. I was able to successfully run both the gene expression and vdj data when I inputted them separately without adding the link column.

 

The submission id is cc6908fe-3fe8-4a1e-8778-2611e65fef61

 

When I tried the multi option, the only stderr output I got was:

Link 'sc5p_v2_hs_B_1k' contains multiple references!

 

When I downloaded the execution log from terra, I noticed in the python script that it does not check for vdj among the various data type options in the multiomics[link_id] column. I think this is might be why my workflow is erroring out.

 

Could you confirm this?

 

Thanks,

 

Wesley

 

Sent from Mail for Windows

 

[Bo Li]

Hi Wesley,

No. Currently cellranger_multi only supports assays with CMO.

Best,

Bo

Bo Li, Ph.D.

Principal Scientist, 

Cell and Tissue Genomics,

Genentech, A Member of the Roche Group

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