10x Genomics Support/Loupe Browser/Analysis/

Cell Ranger ATAC Integration

Cell Ranger ATAC generates .cloupe files for Chromium™ Single Cell ATAC experiments. A .cloupe file is found in the outs folder of a completed Cell Ranger ATAC run, alongside the corresponding fragments.tsv.gz file, which drives cut site visualization.

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 runs 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 ATAC data, and create new subgroups and feature lists on local copies of your dataset. Typical ATAC .cloupe files consume about 50-60 KB of data per cell.

You still need to consult the Cell Ranger ATAC run summary file to view quality control data and other metadata about a particular run; this is not yet available in Loupe Browser.

In addition, Cell Ranger ATAC only generates a .cloupe file for single-species experiments. As a result, you are not able to view multi-species data within Loupe Browser. Instead, you can look at the Web Summary.