10x Genomics Support/Space Ranger/Analysis/

Generating FASTQs

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 the spaceranger mkfastq pipeline or with Illumina's bcl2fastq or BCL Convert software.

Generating FASTQs with spaceranger mkfastq

A thin wrapper around Illumina's bcl2fastq software with a few convenient features for 10x Genomics users