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.

  • $\begingroup$ 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? $\endgroup$
    – M__
    Feb 17, 2020 at 16:18
  • 1
    $\begingroup$ 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? $\endgroup$
    – haci
    Feb 17, 2020 at 20:25
  • $\begingroup$ Perhaps STARsolo is worth looking into. $\endgroup$
    – merv
    Feb 20, 2020 at 4:58
  • $\begingroup$ 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. $\endgroup$ Feb 24, 2020 at 9:23

1 Answer 1


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.

  • $\begingroup$ Do you mind sharing the altered code? And how do you modify the fastqs? $\endgroup$
    – haci
    Feb 17, 2020 at 21:26
  • $\begingroup$ My modifications didn't work, and I strongly recommend not changing code like that unless you understand what you are doing. As to changing the fastqs, you have to understand the format you've got, and what format you want. I use umi_tools to identify the barcodes and their one-offs, and use that list to make replacements. $\endgroup$
    – swbarnes2
    Feb 18, 2020 at 2:03

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