Cell Ranger6.1, printed on 10/13/2024
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. |
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 the vdj_b/ and vdj_t/ 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].