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10x Genomics
Chromium Single Cell ATAC

Cell Ranger ATAC Integration

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

Keeping Local Copies

It is highly recommended that you copy the .cloupe from the pipeline outs folder onto the machine where you run Loupe Cell Browser. Loupe Cell 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 ATAC data, and create new subgroups and feature lists on local copies of your dataset. Typical ATAC .cloupe files consume about 50-60KB of data per cell.

Information Exclusive to the Web Summary View

You will 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 Cell Browser.

In addition, Cell Ranger ATAC will only generate a .cloupe file for single-species experiments. As a result, you will not be able to view multi-species data within Loupe Cell Browser; rather, you will need to look at the Web Summary instead.