For more information, check out our, or our GitHub Wiki. The object serves as a container that contains both data (like the count matrix) and analysis (like PCA, or clustering results) for a single-cell dataset. We next use the count matrix to create a Seurat object. Note that more recent versions of cellranger now also output using the h5 file format, which can be read in using the Read10X_h5() function in Seurat. The values in this matrix represent the number of molecules for each feature (i.e. gene row) that are detected in each cell (column).
The Read10X() function reads in the output of the cellranger pipeline from 10X, returning a unique molecular identified (UMI) count matrix. There are 2,700 single cells that were sequenced on the Illumina NextSeq 500.
