Cell Ranger6.4, printed on 11/29/2023
All pipelines in Cell Ranger 1.3 and later generate .cloupe files for Single Cell 3′ experiments. A .cloupe file will be found in the outs folder of a completed Cell Ranger count, aggr or reanalyze run.
It is highly recommended that you copy the .cloupe from the pipeline outs folder onto the machine where you run Loupe Browser. Loupe Browser makes heavy use of disk I/O, so it will run faster if your file is on local storage, instead of mounted on a network share. This is also good data hygiene; since .cloupe files are editable, it is preferable to leave the original .cloupe with the Cell Ranger data, and create new subgroups and gene lists on local copies of your dataset. Typical .cloupe files consume about 5-10KB of data per cell.
You will still need to consult the Cell Ranger run summary file to view quality control data and other metadata about a particular run; this is not yet available in Loupe Browser.
Cell Ranger 3.0 and later generates a .cloupe file for multi-species ("barnyard") experiments run with a joint reference. This allows Loupe Browser to compute an aggregate transcriptome expression count per cell, enabling easy segmentation by species, or joint analysis for host-virus applications.