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Cell Ranger


10x Genomics
Chromium Single Cell Gene Expression

3' Gene Expression Outputs

The cellranger count pipeline for Gene Expression, Antibody Capture, and CRISPR Guide Capture analysis will each output the files described below in the outs/ directory. There are additional files for Feature Barcode library analysis.

The file hierarchy in the outs/ directory will look like this:

├── analysis
│   ├── clustering
│   ├── diffexp
│   ├── pca
│   ├── tsne
│   └── umap
├── cloupe.cloupe
├── filtered_feature_bc_matrix
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   └── matrix.mtx.gz
├── filtered_feature_bc_matrix.h5
├── metrics_summary.csv
├── molecule_info.h5
├── possorted_genome_bam.bam
├── possorted_genome_bam.bam.bai
├── raw_feature_bc_matrix
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   └── matrix.mtx.gz
├── raw_feature_bc_matrix.h5
└── web_summary.html

Gene Expression library outputs

The subfolder named outs/ will contain the pipeline output files:

File/Folder Description
analysis/ Folder containing the results of graph-based clusters and K-means clustering 2-10; differential gene expression analysis between clusters; and PCA, t-SNE, and UMAP dimensionality reduction. Learn more
cloupe.cloupe A Loupe Browser visualization and analysis file.
filtered_feature_bc_matrix/ Contains only detected cell-associated barcodes in MEX format. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column), as described in the feature-barcode matrix page. This file can be input into third-party packages and allows users to wrangle the barcode-feature matrix (e.g. to filter outlier cells, run dimensionality reduction, normalize gene expression).
filtered_feature_bc_matrix.h5 Same information as filtered_feature_bc_matrix in HDF5 format.
metrics_summary.csv Run summary metrics file in CSV format, described in the Gene Expression metrics page.
molecule_info.h5 Contains per-molecule information for all molecules that contain a valid barcode, valid UMI, and were assigned with high confidence to a gene or Feature Barcode. This file is a required input to run cellranger aggr. Learn more
possorted_genome_bam.bam Indexed BAM file containing position-sorted reads aligned to the genome and transcriptome, as well as unaligned reads, annotated with barcode information. Learn more
possorted_genome_bam.bam.bai Index file for the possorted_genome_bam.bam. In cases where the reference transcriptome is generated from a genome with very long chromosomes (>512 Mbp), Cell Ranger v7.0+ generates a possorted_genome_bam.bam.csi index file instead.
raw_feature_bc_matrix/ Contains all detected barcodes in MEX format. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column), as described in the feature-barcode matrix page.
raw_feature_bc_matrix_h5 Same information as raw_feature_bc_matrix in HDF5 format.
web_summary.html Run summary metrics and charts in HTML format, described in the count web summary page.

Gene Expression and Feature Barcode library outputs

In addition to the files listed above, analysis with Antibody or CRISPR Guide Capture libraries will output your Feature Reference CSV file (feature_reference.csv) and: