Samples: n = 2 (BDR)
Method: 10X Genomics Visium CytAssist
Data generated: November 2023 (R.Bamford, A.Smith, C.Flaxman, S.Leung) Training
If input is raw base call (BCL) files from Illumina sequencers, first demultiplex into fastq using spaceranger mkfastq pipeline/Illumina's bcl2fastq/ BCL Convert software.
If input is fastq, data have already been demultiplexed and can proceed to run spaceranger count.
module load Mamba/4.14.0-0
mamba activate Spatial