Hello, 

Does cellranger count require index fastqs? The doc specifies the output directory of cellranger mkfastq (or csv options), however I have worked with the R1/R2 fastqs generated from another lab without issue. Thanks. 

-Todd
You have likely [seen this page][1] on 10x support site. Sample index files are optional but you do need to have your datafiles named in a specific way (`bcl2fastq`). See section on `My FASTQs are not named like any of the above examples` at end of the page linked.


  [1]: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/fastq-input