Cell Ranger

Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3’ RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.

Cell Ranger 1.2 supports libraries generated by the Chromium Single Cell 3' v1 and v2 reagent kits, whereas Cell Ranger 1.1 and earlier do not support v2 libraries.

Creating your fastq files

First load the cellranger module:

[abc123@login01 ~]$ module load shared cellranger
[abc123@login01 ~]$ SGE_CLUSTER_NAME=SGE cellranger mkfastq --run=./cellranger-tiny-bcl-1.2.0 --samplesheet=cellranger-tiny-bcl-samplesheet-1.2.0.csv --jobmode=sge --mempercore=8

Launch the Cell Ranger pipelines

[abc123@login01 ~]$ SGE_CLUSTER_NAME=SGE cellranger count --id=neuron_9k --transcriptome=/work/data/cellranger-datasets/refdata-cellranger-mm10-1.2.0 --fastqs=/work/abc123/fastqs/neuron_9k --jobmode=sge --mempercore=8

Once the pipelines start up, you will begin to see jobs being submitted to SGE

10619 0.55500 ID.neuron_ abc123 r 02/01/2017 10:27:55 all.q@compute015.cm.cluster 1 
10622 0.55500 ID.neuron_ abc123 r 02/01/2017 10:27:55 all.q@compute015.cm.cluster 1 
10627 0.55500 ID.neuron_ abc123 r 02/01/2017 10:27:55 all.q@compute015.cm.cluster 1 
10635 0.55500 ID.neuron_ abc123 r 02/01/2017 10:27:55 all.q@compute015.cm.cluster 1

-- AdminUser - 01 Feb 2017