Running spaceranger as cluster mode that uses Sun Grid Engine (SGE) as queuing.
There are 2 steps to analyze Spatial RNA-seq data.
spaceranger mkfastq demultiplexes raw base call (
BCL) files generated by Illumina sequencers into FASTQ files.
spaceranger count takes FASTQ files from
spaceranger mkfastq and performs alignment, filtering, barcode counting, and UMI counting.