Creating HTO Count Matrix for Demultiplexing

Question

[fouerghi20]

I have 7 samples that are multiplexed into one pool that I have also run CITE-seq on. I am trying to figure out how to create the HTO count matrix and I have tried to run the CITE-seq-Count python script that is provided as a way to create the HTO count matrix, but since they have updated the latest version, there are some bugs and I can't get the HTO count matrix. Does anyone have experience with how to quantify the HTOs? I am familiar with how to quantify the ADTs, but I have no idea about how to quantify the HTO and thus even begin with my analysis since I have to begin with demultiplexing. Any help would be appreciated, thank you!

[fouerghi20]

Any help regarding this would be appreciated!

Answer 1

[gildas.lepennetier]

Hi there.

I can not help much but you could try the following: - using an previous version of CITE.seq count in python - Figure out why you have some bugs (hard to guess from what you say here)

In my case, work with single cell so I use "cellranger" and provide the CITE-seq information directly to the software. If you have access the the raw data, try using the "cellranger multi"

[fouerghi20]

Hi,

Thank you for the reply! I ended up using cellranger, which replaced the need for this package.