With CellRanger

Find the cellranger OUT directory, it contains an analysis directory and also a subdirectory filtered_gene_bc_matrices. The OUT directory is the one for our tool cbImportCellranger. The tool converts the cellranger files to tab-separated files, then you can run cbBuild on these.

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

pip install scipy

Let’s use an example, the pbmc3k cellranger output files from the 10x website:

rsync -Lavzp genome-test.gi.ucsc.edu::cells/datasets/pbmc3kCellranger/ ./pbmc3kCellranger/ --progress
cbImportCellranger -i pbmc3kCellranger -o cellrangerOut --name pbmc3k_cellranger
cd cellrangerOut
cbBuild -o ~/public_html/cells -p 9999