Cell Ranger - plaisier-lab/mctb_single_cell_symposium GitHub Wiki

Below are links to the main Cell Ranger landing page, mkfastq (the tool to perform BCL conversion), and count (the tool to generate expression matrices for 10X Genomics scRNA-seq data).

• Cell Ranger
  • Cell Ranger mkfastq
  • Cell Ranger count

This is an example of the code used to perform Cell Ranger count on the Lung data that will be used in the workshop.

--id must match the prefix of your fastq file

--sample sets the name of the output folder

cellranger count --id=IPF_Lung1_HWYTFBBXX \
                 --transcriptome=/home/refdata-cellranger-GRCh38-1.2.0 \
                 --fastqs=/scratch/10x_fastq/Fastqs \
                 --sample=Lung1 \
                 --expect-cells=1716 --chemistry=fiveprime```