CellRanger with CITE-seq and hashing

Question

[lic4010]

Hi, I'm trying to run cellranger count, and include, with feature barcoding, fastq files containing antibody-derived tags for CITE-seq and hashtag oligos for cell hashing.

I know it's not supported by 10x but has anybody been able to use the feature barcoding pipeline to analyze these files together to eventually input into Seurat?

Thanks so much.

[igor]

it's not supported by 10x

Cell Ranger can handle CITE-seq and hashtags.

Seurat has a vignette on this topic: https://satijalab.org/seurat/v3.2/multimodal_vignette.html

[Friederike]

Have you tried the analyses described for feature barcoding? Did you run into specific issues?