Cell Ranger7.1, printed on 11/05/2024
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.
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. |
TCR with gamma-delta chains
The cellranger multi pipeline allows users to analyze TCR libraries enriched for gamma (TRG) and delta (TRD) chains. However gamma-delta analysis is not a supported workflow and algorithm performance cannot be guaranteed. TRG/D outputs are located in the |
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].