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Cell Ranger


10x Genomics
Chromium Single Cell Immune Profiling

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 GEMs).

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.


The count/ folder contains the results of 5' single cell gene expression analysis for all GEMs (cell-associated and background). Directory structure is shown here:

├── count
    ├── raw_cloupe.cloupe
    ├── raw_feature_bc_matrix
    ├── raw_feature_bc_matrix.h5
    ├── raw_molecule_info.h5
    ├── unassigned_alignments.bam
    └── unassigned_alignments.bam.bai
File/Folder Description
raw_cloupe.cloupe A Loupe Browser readable file containing data for cell-associated barcodes.
raw_feature_bc_matrix Contains all detected barcodes. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column). The structure of this file is similar to the filtered_feature_bc_matrix file described here.
raw_feature_bc_matrix.h5 Same information as raw_feature_bc_matrix in H5 format.
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]