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.

• Hi Yuriy, could you tell us what how you generated the RNAseq data? That might be important. Also what species/problem you are working with? – M__ Feb 17 '20 at 16:18
• How do the fastq files that belong to a given sample look like, I mean how are they named? Can you share the ls output of a given sample directory? – haci Feb 17 '20 at 20:25
• Perhaps STARsolo is worth looking into. – merv Feb 20 '20 at 4:58
• Hi, It is Smart-Seq2 data that I am hoping to overlap with some 10x data. Regarding the fastq I had to use the mkfastq command. For each sample, I have _R1 _R2 _I1 _I2 files. The naming consists of the sample name, the clone, the lane and the read. – Yuriy Grabovsky Feb 24 '20 at 9:23