Cell Ranger DNA1.1, printed on 11/28/2023
|Analysis software for the 10x Genomics single cell DNA product is no longer supported. Raw data processing pipelines and visualization tools are available for download and can be used for analyzing legacy data from 10x Genomics kits in accordance with our end user licensing agreement without support.|
The cellranger-dna pipeline will generate
.dloupe files that can be found in the
outs folder of a completed run.
Gene-specific functionality, such as searching by gene and viewing gene annotations in the trace, is only available if the reference supplied to cellranger-dna contains gene annotations in a GTF format. For more information on how annotations in the GTF file make it into the Loupe file, consult the cellranger-dna mkref documentation.
.dloupe file encodes the same tree structure, copy numbers and heterogeneity as the other output files in the pipeline. However, the file
stores a quantized, approximated read depth per bin in order to save disk space. For more information, see Technical Details.
You will still need to consult the Cell Ranger DNA run summary file to view quality control data and other metadata about a particular run; this is not available in Loupe scDNA Browser.
It is highly recommended that you copy the
.dloupe file from the pipeline
outs folder onto the machine where you
will run Loupe scDNA Browser. Loupe scDNA Browser makes heavy use of disk I/O, so it will run faster if your file is
on a local drive as opposed to on a mounted network share. Typical
.dloupe files consume about 250-300KB of disk
space per cell, though that figure also depends on copy number variability and genome size.