The spaceranger mkfastq pipeline is deprecated and will be removed in a future release. Please use Illumina’s BCL Convert to generate Space Ranger-compatible FASTQ files. For detailed guidance, refer to the Demultiplexing with Illumina Software page.
Raw base call (BCL) files from Illumina sequencers must be demultiplexed into FASTQ files that the spaceranger count pipeline requires as input. If you have obtained FASTQs from a sequencing service provider, an online database, or elsewhere, the data have already been demultiplexed, and you can proceed to run spaceranger count. Otherwise, you have the option of demultiplexing with Illumina's bcl2fastq or BCL Convert software.