CellRanger with CITE-seq and hashing
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13 months ago
lic4010 ▴ 10

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.

CellRanger Hashing CITE-seq 10x Genomics • 1.5k views
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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

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

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