
For more information on telemetry in Cell Ranger ARC and how to disable it, see [this page](/support/software/cell-ranger-arc/latest/tutorials/cr-arc-pipeline-telemetry).

```
annotated_cells
atac_current_mean_dup_count
atac_frac_fragments_in_cells
atac_frac_fragments_nfr
atac_frac_fragments_nuc
atac_frac_fragments_overlapping_peaks
atac_frac_fragments_overlapping_tss
atac_frac_fragments_usable_ontarget
atac_frac_mapped_confidently
atac_frac_primary_genome_in_peaks
atac_frac_valid_barcode
atac_frac_waste_exclusions_gel_bead_doublet_total
atac_median_fragments_per_cell
atac_median_per_cell_targeted_unique_fragments
atac_median_per_cell_targeted_unique_fragments_at_1.3_mean_dup_count
atac_median_per_cell_unique_fragments
atac_median_per_cell_unique_fragments_at_1.3_mean_dup_count
atac_num_fragments
atac_samples_count
atac_total_peaks_detected
atac_tss_enrichment_score
avx
bin_filesystem
cgroup_memory_hard_limit
cgroup_memory_soft_limit
check_library_compatibility
container
core_hours
cores_per_socket
cpu_mfg
create_bam
custom_peaks
disk_hwm
distro
error
event_count
failed_stage
feature_linkage_max_dist_mb
gex_exclude_introns
glibc
jobmode
joint_filtered_matrix_barcodes_count
joint_filtered_matrix_features_count
joint_filtered_matrix_nonzero_entries_count
joint_raw_matrix_barcodes_count
joint_raw_matrix_features_count
joint_raw_matrix_nonzero_entries_count
kernel
memory
min_atac_count
min_gex_count
normalize
nosecondary
num_feature_linkages
pipestance_filesystem
process_ulimit
processor_count
rna_bc_bases_with_q30_frac
rna_filtered_bcs_transcriptome_union
rna_good_bc_frac
rna_good_umi_frac
rna_multi_cdna_pcr_dupe_reads_frac
rna_r1_length
rna_r2_length
rna_read_bases_with_q30_frac
rna_reads_per_cell
rna_total_read_pairs
rna_umi_bases_with_q30_frac
rna_unprocessed_read_pairs
runtime
socket_count
subcommand
transparent_huge_pages
utime
vmem_ulimit
```


Telemetry Metrics Collected by Cell Ranger ARC Pipelines

Cell Ranger ARC is an advanced analytical suite designed for the Chromium Single Cell Multiome ATAC + Gene Expression sequencing. It provides in-depth analysis of gene expression and chromatin accessibility at a single cell level, uniquely linking these aspects for enhanced genomic understanding.

Overview

Getting Started

Download Center

Analysis

Tutorials

Algorithms

Advanced

Troubleshooting

Release Notes

Datasets

Loupe Browser

Cell Ranger ARC

A tutorial on using Cell Ranger ARC mkref to create a reference for Rattus norvegicus

Custom Reference for Rat

Understand pipeline telemetry data collection and learn how to disable it if needed

Cell Ranger ARC Pipeline Telemetry

Learn more about input files required to run Cell Ranger ARC

Inputs

Generating FASTQs (mkfastq)

Specifying FASTQs

FASTQs with Illumina Software

Custom Reference (mkref)

Learn more about how to run Cell Ranger ARC

Running Pipelines

Command Line Arguments

Analyzing GEX + ATAC (count)

Aggregating Multiple Samples (aggr)

Custom Analysis (reanalyze)

Cell Type Annotation

Learn more about the output files generated by Cell Ranger

Outputs

Web Summary

Secondary Analysis

Feature-Barcode Matrices

Summary CSV

Per Barcode QC Metrics

ATAC Barcoded BAM

ATAC Fragments

ATAC Peaks

ATAC Peak Annotations

ATAC Transposition Counts

GEX Barcoded BAM

GEX Molecule Info (H5)

HDF5 Feature Barcode Matrix Format

Cell Type Annotations

What is Cell Ranger ARC?

<Flex style={{
  flexDirection: 'column',
  gap: '0.5rem'
}}><div><Text as={'span'} size={'small'} weight={'medium'}>{'Starting with v2.1, anonymized telemetry data is collected and sent to 10x Genomics. '}</Text><Anchor href={'https://www.10xgenomics.com/support/software/cell-ranger-arc/latest/tutorials/cr-arc-pipeline-telemetry'}><Text as={'span'} color={'inherit'} size={'small'} weight={'medium'}>{'Learn how to disable.'}</Text></Anchor></div><Text as={'p'} size={'small'} weight={'medium'}>The cellranger-arc mkfastq pipeline is deprecated and will be removed in a future release. Please use Illumina’s BCL Convert to generate compatible FASTQ files.</Text></Flex>

We provide resources from protocols, user guides, and free-to-use analysis tools

Algorithms overview

Advanced pipeline content for Cell Ranger ARC.

View the latest updates to Cell Ranger ARC.

Browse Q&As from the 10x Genomics support team.

Access free public Chromium data from 10x Genomics.

Loupe Browser is a desktop application that allows you to interactively visualize data.

Miscellaneous