STARsolo and Cellranger (v8) differences in estimating number of cells

[angelasanzo]

Hi there,

Thank you for developing STARsolo. I’ve been using it for a while, but I’ve encountered an issue while working with cells that have a low number of reads as they are quite fragile. After comparing the results with CellRanger v8, I noticed that STARsolo is estimating about half the number of cells compared to CellRanger v8 (7000 to 3000 cells). Currently, we are sequencing using GEM-X (chemistry 3'v4).

I suspect that there might be some parameter optimization I'm missing, so I’d like to share my current approach and get your thoughts on potential improvements.

Here’s the command I’ve been using:

/opt/STAR-2.7.9a/bin/Linux_x86_64/STAR
--runThreadN 20
--genomeDir /home/data/human/GRCh38/STAR-2.7.9a
--readFilesIn $reads
--runDirPerm All_RWX
--readFilesCommand zcat
--outSAMtype None
--soloType CB_UMI_Simple
--soloCBwhitelist /home/output/3M-3pgex-may-2023.txt
--soloBarcodeReadLength 28
--soloCBstart 1
--soloCBlen 16
--soloUMIstart 17
--soloUMIlen 12
--soloStrand Reverse
--soloUMIdedup 1MM_CR
--soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts
--soloUMIfiltering MultiGeneUMI_CR
--soloCellFilter EmptyDrops_CR
--clipAdapterType CellRanger4
--outFilterScoreMin 30
--soloFeatures Gene GeneFull Velocyto

I would greatly appreciate any suggestions or adjustments to the parameters that might help improve cell recovery for low-read samples.

Thanks in advance for your help.

Angela