CiteSeq Tutorial


I’ve been following the CITESeq tutorial using muon.

I am using a data set that has RnaSeq for PBMCs and 10 CiteSeq epitopes (no controls). The epitopes are immune cell specific such as Cd4 CD8 which only a subset of the PBMCs will express.

I’ve already processed and QC’d my RNA data, and generated the MuonData for this. I’ve also made the raw MuonData using the unfiltered data files.

Following the tutorial I calculated the Log10UMI for the genes and loaded this in the rna.obs

What I am unclear on is how I should calculate the settings for the

empty_counts_range=(1.5, 2.8)

When using the DSB function.

Following applying the dsb function I still don’t have a clear positive and negative population for my CITEseq epitopes.

Some advice on optimising this would be very appreciated.

Is it better to run the dsb on the cell ranger filtered matrices or on an initial QC’d rna data set which has removed high mito counts and doublets etc….