Cell Ranger7.1, printed on 11/05/2024
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: