Using cellranger for non-10x data I'm trying to use cellranger to mkfastq and then count and 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.
Possible?  Sure.  Your biggest problem is that 10x is expecting barcodes from its whitelist.  I used to alter the python scripts to accept a 'new' kind of chemistry where the barcodes and umi lengths matched what I had, but I found that my modifications stopped working when the version updated,  and I couldn't figure it out, so I started modifying fastqs instead.