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cellgeni / STARsolo

wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq
GNU General Public License v3.0
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Can I use the STARsolo for the multiome data? #6

Closed kkonoo closed 1 year ago

kkonoo commented 1 year ago

Hi there,

I have overloaded multiome data (with >20k cells), so I don't want to use cell ranger arc, which has a limit in the number of cells to be called. Can I use the STARsolo for the multiome data? If so, how can I use it?

Best, E

apredeus commented 1 year ago

Hi E, I don't think you can do ATAC-seq processing with STARsolo (even in Cell Ranger they use bwa + macs2 to map the genomic reads and call peaks). But if you're only interested in the RNA part of the multiome, then a normal 10x workflow (and using GeneFull output) should work well.