Cell Ranger ARC6.3, printed on 06/05/2023
If you have used Loupe Browser to analyze Gene Expression or ATAC data, exploring Multiome data will feel familiar in some ways. The Cell Ranger ARC algorithm documentation covers algorithms and analysis in more detail, but in short, here are some key things to remember when looking at Multiome ATAC + Gene Expression data.
Both ATAC and Gene Expression data are available for the same cells. This means that many types of features are available for the same cell, including UMI counts per cell, cut sites per cell, transcription factor motif z-scores, and aggregate features (see below).
A pair of t-SNE and UMAP projections are computed from Gene Expression and ATAC data, respectively.
Peaks are genomic regions where there were significant upticks in fragment cut sites, which indicate regions of open chromatin. They are named by their location (e.g., "chr1:10244-10510")
Unlike genes, peaks are likely to be different between different datasets, or even the same dataset sequenced at different depths.
There are typically more distinct peaks than there are genes.
The dynamic range of gene expression per cell is typically much wider than the dynamic range of cut sites per peak per cell.
The main new datatype in a Multiome ATAC + Gene Expression dataset is Feature Linkages, which are correlations between gene expression and patterns of open chromatin across all cells in the dataset. Linked features can be gene-to-peak, or peak-to-peak. Features must be within a megabase of each other to be linked.
In addition to genes and peaks, there are several aggregate feature types which can also be used to differentiate cells:
A Single Cell Multiome ATAC + Gene Expression dataset takes up several times as much disk space (per cell) than a Single Cell Gene Expression dataset, and a small amount more than Single Cell ATAC datasets.
To see fragment locations per cluster in high resolution, you need access to the
for that run, generated by the Cell Ranger ARC pipeline. These files are typically several times larger than
.cloupe file, which is why they are not bundled. You can either specify the location of this file on a locally mounted file system, or on the web via a URL.