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Cell Ranger


Loupe

10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger7.1 (latest), printed on 12/24/2024

Barcode Enabled Antigen Capture for T Cells (BEAM-T)

A tutorial on running the cellranger multi pipeline with an example BEAM-T dataset

Learning objectives

In this tutorial, you will:

Prerequisites

To follow along, you must:

Chromium Single Cell 5’ Barcode Enabled Antigen Mapping

The Chromium Single Cell 5’ Barcode Enabled Antigen Mapping (BEAM) technology offers a scalable approach for mapping a V(D)J receptor to a target antigen by enabling the detection of gene expression profiles, paired V(D)J receptors, and signal from a bound antigen from the same single cell. All of these libraries, generated from a single GEM well, can be analyzed together with Cell Ranger v7.1 or later using the cellranger multi pipeline.

Example dataset

We will work with the 5k Human A0201 | B0702 PBMCs (BEAM-T) dataset.

Download example FASTQs

Open up a terminal window. You may log in to a remote server or choose to perform the compute on your local machine. Refer to the System Requirements page for details.

In the working directory, create a new folder called beam-t and cd into that folder:

mkdir beam-t
cd beam-t

Download the input FASTQ files:

curl -O https://cf.10xgenomics.com/samples/cell-vdj/7.1.0/5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex/5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex_fastqs.tar

A file named 5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex_fastqs.tar should appear in your directory when you list files with the ls -lt command.

Uncompress the FASTQs:

tar -xf 5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex_fastqs.tar

You should now see a folder called 5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_fastq

cd 5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_fastq
ls

The folder contains three subfolders with library-specific FASTQS files: antigen_capture, gex, and vdj.

Navigate back to the working directory:

cd ..

Double check you are in the correct directory by running the ls command; the working directory should have the FASTQs 5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_fastqs folder.

Download example Feature Reference CSV

Download the Feature Reference CSV available for this example dataset.

curl -O https://cf.10xgenomics.com/samples/cell-vdj/7.1.0/5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex/5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex_count_feature_reference.csv

To view the contents of the Feature Reference CSV, open it in your text editor of choice (e.g., nano)

nano 5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex/5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex_count_feature_reference.csv

The contents should look like this:


id,name,read,pattern,sequence,feature_type,mhc_allele
Flu_A0201,Flu_A0201,R2,^(BC),GATTGGCTACTCAAT,Antigen Capture,HLA-A*02:01
CMV_B0702,CMV_B0702,R2,^(BC),CGGCTCACCGCGTCT,Antigen Capture,HLA-B*07:02
negative_control_A0201,negative_control_A0201,R2,^(BC),CTATCTACCGGCTCG,Antigen Capture,HLA-A*02:01
negative_control_B0702,negative_control_B0702,R2,^(BC),CATGTCTACGTTAAG,Antigen Capture,HLA-B*07:02

Since this is a BEAM-T (TCR Antigen Capture) dataset, the Feature Reference CSV contains the additional mhc_allele column. The BEAM-Ab tutorial guides you through analyzing a BCR Antigen Capture dataset.

When working with your own dataset, you must customize this file for your experiment. Learn more about the Feature Reference CSV.

Download the reference transcriptome and V(D)J reference

Download the pre-built human reference transcriptome to the working directory (beam-t/) and uncompress it:

curl -O https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz
tar -xf refdata-gex-GRCh38-2020-A.tar.gz

Next, download the pre-built V(D)J reference to the working directory and uncompress it:

curl -O https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0.tar.gz
tar -xf refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0.tar.gz

Download or create a multi config CSV

In your working directory, create a new CSV file called 5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex_config.csv using your text editor of choice. For example, you can create a file with nano using this command:

nano 5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex_config.csv

Copy and paste this text into the newly created file and customize the /path/to/... part of file paths:

[gene-expression]
ref,/path/to/references/refdata-gex-GRCh38-2020-A

[feature]
ref,/path/to/feature_references/5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex_count_feature_reference.csv

[vdj]
ref,/path/to/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0

[libraries]
fastq_id,fastqs,lanes,feature_types
beamt_human_A0201_B0702_pbmc_ag,/path/to/fastqs/5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_fastqs/antigen_capture,1|2,Antigen Capture
beamt_human_A0201_B0702_pbmc_vdj,/path/to/fastqs/5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_fastqs/vdj,1|2,VDJ-T
beamt_human_A0201_B0702_pbmc_gex,/path/to/fastqs/5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_fastqs/gex,1|2,Gene Expression

[antigen-specificity]
control_id,mhc_allele
negative_control_A0201,HLA-A*02:01
negative_control_B0702,HLA-B*07:02

Use your text editor's save command to save the file. In nano, save by typing → → .

A customizable multi config CSV template is available for download on the example dataset page, under the Input Files tab.

Set up the directory for running multi

Once you have all the necessary files, make a new directory called runs/ in your beam-t working directory:

mkdir runs/
cd runs/

You will run cellranger multi in the runs/ directory.

Set up the command for running multi

After downloading/creating the FASTQ files, Feature Reference CSV, reference transcriptome, and V(D)J reference, you are ready to run cellranger multi.

Print the usage statement to get a list of all the options:

cellranger multi --help

The output should look similar to:

user_prompt$ cellranger multi --help
cellranger-multi
Analyze multiplexed data or combined gene expression/immune profiling/feature
barcode data

USAGE:
    cellranger multi [FLAGS] [OPTIONS] --id  --csv 
 
FLAGS:
        --dry            Do not execute the pipeline. Generate a pipeline
                         invocation (.mro) file and stop
        --disable-ui     Do not serve the web UI
        --noexit         Keep web UI running after pipestance completes or fails
        --nopreflight    Skip preflight checks
    -h, --help           Prints help information

OPTIONS:
        --id                A unique run id and output folder name [a-zA-Z0-
                                9_-]+
        --description     Sample description to embed in output files
                                [default: ]
        --csv              Path of CSV file enumerating input libraries and
                                analysis parameters
        --jobmode         Job manager to use. Valid options: local
                                (default), sge, lsf, slurm or path to a
                                .template file. Search for help on "Cluster
                                Mode" at support.10xgenomics.com for more
                                details on configuring the pipeline to use a
                                compute cluster [default: local]
        --localcores       Set max cores the pipeline may request at one
                                time. Only applies to local jobs
        ....

Options used in this tutorial

Option Description
--id The id argument must be a unique run ID. We will call this run HumanB_Cell_multi based on the sample type in the example dataset.
--csv Path to the multi config CSV file enumerating input libraries and analysis parameters. Your multi_config.csv file is in the working directory. When executing cellranger multi from the runs directory, the relative path should be: ../multi_config.csv

Run the multi pipeline

From within the beam-t/runs/ directory, run cellranger multi

/path/to/cellranger-7.1.0/cellranger multi --id=beam-t-run --csv=../5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex_config.csv

The run begins similarly to this:

user_prompt$ cellranger multi --id=beam-t-run --csv=/jane.doe/beam-t/multi_config.csv
Martian Runtime - v4.0.10
2023-06-15 11:44:24 [jobmngr] WARNING: configured to use 334GB of local memory, but only 194.9GB is currently available.
Serving UI at http://bespin3.fuzzplex.com:34513?auth=-Sm5gsg6_G8FjcUX0_YD5J8SYoBODz4IWoVIK9ec0jg

Running preflight checks (please wait)...
2023-06-15 11:44:33 [runtime] (ready)           ID.beam-t-run.SC_MULTI_CS.PARSE_MULTI_CONFIG
2023-06-15 11:44:33 [runtime] (run:local)       ID.beam-t-run.SC_MULTI_CS.PARSE_MULTI_CONFIG.fork0.chnk0.main
2023-06-15 11:44:56 [runtime] (chunks_complete) ID.beam-t-run.SC_MULTI_CS.PARSE_MULTI_CONFIG
2023-06-15 11:44:56 [runtime] (ready)           ID.beam-t-run.SC_MULTI_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX
2023-06-15 11:44:56 [runtime] (run:local)       ID.beam-t-run.SC_MULTI_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX.fork0.chnk0.main
....

When the output of the cellranger multi command says, “Pipestance completed successfully!”, the job is done:

      web_summary:      /jane.doe/beam-t/runs/beam-t-run/outs/per_sample_outs/beam-t/web_summary.html
      metrics_summary:  /jane.doe/beam-t/runs/beam-t-run/runs/beam-t/outs/per_sample_outs/beam-t/metrics_summary$
  }
 
Waiting 6 seconds for UI to do final refresh.
Pipestance completed successfully!
 

Generate and explore the output files

A successful cellranger multi run produces a new directory called beam-t-run (based on the --id flag specified during the run). The contents of the beam-t-run directory:

.
├── beam-t-run
│   ├── beam-t.mri.tgz
│   ├── _cmdline
│   ├── _filelist
│   ├── _finalstate
│   ├── _invocation
│   ├── _jobmode
│   ├── _log
│   ├── _mrosource
│   ├── outs
│   ├── _perf
│   ├── _perf._truncated_
│   ├── SC_MULTI_CS
│   ├── _sitecheck
│   ├── _tags
│   ├── _timestamp
│   ├── _uuid
│   ├── _vdrkill
│   └── _versions

The outs/ directory contains all important output files generated by the cellranger multi pipeline:

── runs
    └── beam-t-run
          └──outs
             ├── config.csv
             ├── multi
             │   ├── count
             │   │   ├── feature_reference.csv
             │   │   ├── raw_cloupe.cloupe
             │   ├── raw_feature_bc_matrix
             │   │   ├── raw_feature_bc_matrix.h5
             │   │   ├── raw_molecule_info.h5
             │   │   ├── unassigned_alignments.bam
             │   │   └── unassigned_alignments.bam.bai
             │   └── vdj_t
             │       ├── 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
             ├── per_sample_outs
             │   └── beam-t
             │       ├── antigen_analysis
             │       ├── count
             │       ├── metrics_summary.csv
             │       ├── vdj_t
             │       └── web_summary.html
             └── vdj_reference
                 ├── fasta
                 │   ├── donor_regions.fa
                 │   └── regions.fa
                 └── reference.json

Next steps