With Cell RangerΒΆ

Find the cellranger OUT directory, it should contain an analysis directory and a subdirectory filtered_gene_bc_matrices. The OUT directory will be the input for our tool cbImportCellranger. The tool converts the cellranger files to ones formatted for cbBuild.

As we are reading Cell Ranger mtx files, we need the scipy package (add --user if you are not the admin on your machine):

pip install scipy

The example below use the pbmc3k cellranger output files from the 10x website. First, download the files with the command:

rsync -Lavzp genome-test.gi.ucsc.edu::cells/datasets/pbmc3kCellranger/ ./pbmc3kCellranger/ --progress

Next, run cbImportCellranger to convert the cellranger files into something that can be used to build a cell browser:

cbImportCellranger -i pbmc3kCellranger -o cellrangerOut --name pbmc3k_cellranger

The -i option specifies the input cellranger directory and the -o option specifies a name for the output directory. You can use the -n option to change the dataset name in the cell browser; if it is not specified, it will default to the output directory name.

Lastly, go into the cellrangerOut directory and run cbBuild to create a cell browser:

cd cellrangerOut
cbBuild -o ~/public_html/cells -p 9999