Cell Ranger7.0, printed on 12/17/2024
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 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. |
|
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. |
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