Demultiplexing Samples With Contaminated Hashtag
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4 weeks ago
fouerghi20 ▴ 30

I have used the Satija lab's cell hashing approach where we have hashed 8 conditions together. Unfortunately, it seems like one of the antibodies we used was binding nonspecifically to cells that expressed the other hashing conditions according to the ridge plots I generated. Has anyone encountered this situation before where they have a contaminated hashtag so the assignment of doublets, singlets and negatives by the HTODemuxlet is influenced by that and how do you account for this contamination? Can I scale back this hashtag's expression? any help would be appreciated

scRNAseq seurat demultiplexing • 89 views

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