I'm trying to use cellranger to
mkfastq and then
aggregate single-cell data. This data was not generated using 10x Genomics RNASeq.
When I run
count, cellranger fails to auto id the chemistry and crashes out. Is it possible to wrangle the data into the cellranger method or should I look elsewhere. I'd ideally like to use the same method for all my single-cell data but not all of it is 10x.