10x Genomics
Chromium Single Cell Gene Expression
Cell Ranger3.0, printed on 12/22/2024
Cell Ranger Integration
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.
| A .cloupe file will not be created for pipelines run against multi-species references, such as human-vs-mouse system validation experiments. If you are looking to create a reference that merges genes from multiple species into a single gene-barcode matrix, which will trigger .cloupe generation, please contact support@10xgenomics.com. |
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 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.
Creating Categories through cellranger aggr
When combining multiple samples into a single dataset with the cellranger aggr pipeline, you can assign categories and values to individual samples by adding columns to the cellranger aggr input spreadsheet. These category assignments propagate into Loupe Cell Browser, where you can view them, and determine genes that drive differences within samples. For example, the following spreadsheet was used to aggregate the tutorial dataset:
| A | B | C | |
|---|---|---|---|
| 1 | library_id | molecule_h5 | AMLStatus |
| 2 | AMLNormal1 | /path/to/AMLNormal1/molecule_info.h5 | Normal |
| 3 | AMLNormal2 | /path/to/AMLNormal2/molecule_info.h5 | Normal |
| 4 | AMLPatient | /path/to/AMLPatient/molecule_info.h5 | Patient |
Any columns in addition to 'library_id' and 'molecule_h5' will be converted into categories, and the cells in each sample will be assigned to one of the values in that category.
Information Exclusive to the Web Summary View
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 Cell Browser.
In addition, Cell Ranger will only generate a .cloupe file for single-transcriptome experiments. As a result, you will not be able to view barnyard data within Loupe Cell Browser; rather, you will need to look at the Web Summary instead.
Generating .cloupe files from Cell Ranger 1.2 pipelines
If you have data from a Cell Ranger 1.2 pipeline, you can generate a .cloupe file for it using the cellranger mkloupe command from Cell Ranger 1.3 or later.
After downloading and installing the latest version of Cell Ranger, run the following on a Cell Ranger 1.2 output folder:
$ cellranger mkloupe --id=<sample id> --type=<either count or aggr> --path=<path to your cellranger output folder>
Generating .cloupe files for Cell Ranger 1.1 and earlier is not supported.