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
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. |
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: