Running spaceranger as cluster mode that uses Sun Grid Engine (SGE) as queuing.

There are 2 steps to analyze Spatial RNA-seq data.

Step 1: spaceranger mkfastq demultiplexes raw base call (BCL) files generated by Illumina sequencers into FASTQ files.
Step 2: spaceranger count takes FASTQ files from spaceranger mkfastq and performs alignment, filtering, barcode counting, and UMI counting.