10XGenomics CellRanger quick start

The first step is to download the cellranger and reference genome tarballs. These are available from the 10XGenomics dowload page. Note that you need to sign in with your email to agree to the EULA, and then a token is generated. While this precludes putting direct links here, they are nice enough to provide customized curl commands to make things easy.

Also required is Illumina’s bcl2fastq, which takes a while to build:

wget ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/bcl2fastq2-v2-20-0-tar.zip
unzip bcl2fastq2-v2-20-0-tar.zip
tar -zxvf bcl2fastq2-v2.20.0.422-Source.tar.gz  
export INSTALL_DIR=~/local
cd bcl2fastq
./src/configure --prefix=~/local
make
make install

Now unarchive the cell ranger suite.

tar -zxvf cellranger-2.1.0.tar.gz

And then move the cellranger-2.1.0 directory to somewhere on your path, and/or edit your .bashrc file to add its location to your path.

Move the reference genome data tarball somewhere convenient (I use ~/local/srv/seq/chromium), then unarchive it:

tar -zxvf refdata-cellranger-GRCh38-1.2.0.tar.gz

Finally, run the test:

cellranger testrun --id=tiny