10x Genomics Support/Cell Ranger 7.2/Analysis/

Cell Ranger multi Raw (Unfiltered) Outputs

The multi/ directory is produced after the 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 not 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
  • vdj_t or vdj_t_gd
  • vdj_b

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/FolderDescription
feature_reference.csvCopy of the input Feature Reference CSV.
raw_cloupe.cloupeA Loupe Browser readable file containing data for cell-associated barcodes.
raw_feature_bc_matrixFolder 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_molecule_info.h5Contains 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.bamAlignments of reads from background barcodes (i.e. barcodes not assigned as cells).
unassigned_alignments.bam.baiCompanion 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.
Important
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 outs/per_sample_outs/mySample/vdj_t_gd folder. Output files in the vdj_t_gd folder are similar to those of 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/FolderDescription
all_contig_annotations.bedHigh-level and detailed annotations of each contig in .bed format.
all_contig_annotations.csvHigh-level and detailed annotations of each contig in .csv format. One contig per row.
all_contig_annotations.jsonHigh-level and detailed annotations of each contig in .json format.
all_contig.bamContains alignment of reads that have been assembled into contigs against the V(D)J reference.
all_contig.bam.baiCompanion file to the all_contig.bam that serves as an external index.
all_contig.fastaFASTA format sequence for each assembled contig in the V(D)J library.
all_contig.fasta.faiCompanion file to the all_contig.fasta.fai that serves as an external index.
all_contig.fastqFASTQ 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.