CellRanger with CITE-seq and hashing
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.
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Cell Ranger can handle CITE-seq and hashtags.
Seurat has a vignette on this topic: https://satijalab.org/seurat/v3.2/multimodal_vignette.html
Have you tried the analyses described for feature barcoding? Did you run into specific issues?