The final "cellranger count" output yields gene expression matrices for each sample that contain the UMI counts per gene, per cell barcode. The results also include summary files with summary metrics describing sequencing quality along with secondary analysis output that includes PCA, t-SNE and UMAP plots; details on grouping of cells with similar expression profiles (clustering) and features differentially expressed in each cluster relative to all other clusters. The output ".cloupe" files are used for visualization and analysis in Loupe Browser.