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Cell Ranger


Loupe

10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger7.1, printed on 12/25/2024

Cell Ranger multi: Raw Outputs

The multi/ directory is produced after a successful execution of the multi pipeline and contains raw data, i.e., data from all barcodes (cells + background). Refer to the Filtered Outputs page to learn about filtered outputs (excludes background barcodes that have no been called as cells).

Contents of the following folders located within the multi/ directory are described here. Click on the folder name below or scroll down to learn more.

count

The count/ folder contains the results of 5' Single Cell Gene Expression (GEX) and Feature Barcode libraries for all GEMs (cell-associated and background). The directory structure is shown here:

    
├── count    
    ├── feature_reference.csv
    ├── raw_cloupe.cloupe
    ├── raw_feature_bc_matrix
        ├── barcodes.tsv.gz
        ├── features.tsv.gz
        └── matrix.mtx.gz
    ├── raw_feature_bc_matrix.h5
    ├── raw_molecule_info.h5
    ├── unassigned_alignments.bam
    └── unassigned_alignments.bam.bai
File/Folder Description
feature_reference.csv Copy of the input Feature Reference CSV.
raw_cloupe.cloupe A Loupe Browser readable file containing data for cell-associated barcodes.
raw_feature_bc_matrix Folder contains gzipped TSV files. In the features.tsv.gz, feature and barcode sequences correspond to row and column indices, respectively. The third column identifies the type of feature, which will be one of Gene Expression, Antibody Capture, CRISPR, Antigen Capture, or CUSTOM, depending on the feature type. Contains all detected barcodes. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column). All TSV files are described here.
raw_feature_bc_matrix.h5 Same information as raw_feature_bc_matrix in H5 format.
raw_molecule_info.h5 Contains per-molecule information for all molecules that contain a valid barcode, a valid UMI, and were assigned with high confidence to a gene or Feature Barcode. Learn more.
unassigned_alignments.bam Alignments of reads from background barcodes (i.e. barcodes not assigned as cells).
unassigned_alignments.bam.bai Companion file to the unassigned_alignments.bam that serves as an external index. In cases where the reference transcriptome is generated from a genome with very long chromosomes (>512 Mbp), Cell Ranger v7.0+ generates an unassigned_alignments.bam.csi index file instead.

vdj (_t/_b)

The vdj_t/ and vdj_b/ folders contain the results of V(D)J immune profiling analysis for all barcodes (cells-associated and background) in the T cell and B cell libraries, respectively. The output file names and file structure in these folders are identical, and are only described once:

├── vdj_b
    ├── all_contig_annotations.bed
    ├── all_contig_annotations.csv
    ├── all_contig_annotations.json
    ├── all_contig.bam
    ├── all_contig.bam.bai
    ├── all_contig.fasta
    ├── all_contig.fasta.fai
    └── all_contig.fastq
File/Folder Description
all_contig_annotations.bed High-level and detailed annotations of each contig in .bed format.
all_contig_annotations.csv High-level and detailed annotations of each contig in .csv format. One contig per row.
all_contig_annotations.json High-level and detailed annotations of each contig in .json format.
all_contig.bam Contains alignment of reads that have been assembled into contigs against the V(D)J reference.
all_contig.bam.bai Companion file to the all_contig.bam that serves as an external index.
all_contig.fasta FASTA format sequence for each assembled contig in the V(D)J library.
all_contig.fasta.fai Companion file to the all_contig.fasta.fai that serves as an external index.
all_contig.fastq FASTQ format sequence for each assembled contig in the V(D)J library.

Visit the Filtered Outputs page to work with filtered data containing only cell-associated barcodes.

If you have any questions or feedback, please contact [email protected].