Low overlap between cell barcodes and hashtag barcodes

[mary77]

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]

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

[mary77]

Hey @Hoohm
Yes, same person.