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Hoohm / CITE-seq-Count

A tool that allows to get UMI counts from a single cell protein assay
https://hoohm.github.io/CITE-seq-Count/
MIT License
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Low overlap between cell barcodes and hashtag barcodes #159

Open mary77 opened 2 years ago

mary77 commented 2 years ago

We are trying to demultiplex our samples using Cite-seq but we are getting low overlap between cell barcodes and hashtag barcodes. We used the same pipeline on our previous experiment and didn't have this issue. Here is a summary of our experiment :

Experimental library summary: • Nuclei samples • Nuclei HTO staining • Added HTO cDNA PCR additive primer (V1) • Used 10x dual index plate TT for both HTO library and transcriptome • Not great overlap at demultiplexing step post sequencing

Could you please help us to resolve this issue?

Hoohm commented 2 years ago

Hey @mary77 just checking that you are the same person I'm talking to via email.

mary77 commented 2 years ago

Hey @Hoohm Yes, same person.