With Cell Ranger¶
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