# cellranger

## Summary

+ **Module Name:** cellranger
+ **Support Level:** Primary Support
+ **Software Access Level:** Open Access
+ **Home Page:** https://www.10xgenomics.com/support/software/cell-ranger/latest

## Software Description

CellRanger is a software package from 10X Genomics that is used to demultiplex 10X 
Genomics sequencing FASTQ files to produce a cell-by-gene counts matrix containing the 
expression of each gene for each cell barcode, along with a  quality report detailing the 
number of valid cell barcodes that were found, median numbers of genes and transcripts per cell, 
and read alignment statistics to the genome. MSI provides selected reference files that are 
compatible with cellranger in the [bioref database](https://msi.umn.edu/consulting-and-research/bioinformatics-guides/bioref) in this directory:

`/common/bioref/cellranger_10x/`

## General Linux

Depending on where you are working, there may be more than one version of CellRanger available.
To see which modules are available for loading you can run:

`module avail cellranger`

This will provide a list of all versions of the package, shown as cellranger/<version>.

To load a specific module for use in a Linux environment, run the command:

`module load cellranger/<version>`

For example, you can use the command `module load cellranger/10.0.0` to load version 10.0.0 
which is the current version available on our system.

To launch the package and view the help menu after it is loaded, use the command:

`cellranger -h`


## Example SBATCH Script
The following is an example job script (cellranger_count.sbatch) to perform cell demultiplexing with CellRanger on 10X Genomics
3' or 5' Gene Expression (GEX) data.
```
############cellranger_count.sbatch############

#!/bin/bash
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 24
#SBATCH --mem=128gb
#SBATCH -t 96:00:00
#SBATCH -p msismall
#SBATCH -A YOUR_GROUP
#SBATCH --mail-user=YOUR_EMAIL@umn.edu
#SBATCH --mail-type=ALL
#SBATCH -e cellranger_%j.err
#SBATCH -o cellranger_%j.out

# Load the cellranger module
module load cellranger/10.0.0

# The following cellranger command will align sequencing reads to the human GRCh38 transcriptome
# reference built by 10X Genomics (v2024) and demultiplex cells.

FASTQ_DIR="/path/to/your/FASTQ/folder/"      # The path to your folder of FASTQ files
SAMPLE="sample1"                             # The unique sample name prefix on your FASTQ files
ID="cellranger_${SAMPLE}"                    # The name of the cellranger output folder

cellranger count \
--id=${ID} \
--sample=${SAMPLE} \
--transcriptome=/common/bioref/cellranger_10x/refdata-gex-GRCh38-2024-A/ \
--fastqs ${FASTQ_DIR} \
--chemistry auto \
--create-bam true \
--localcores=24 \
--localmem=128

```