
<LinkableSection id={"cell-ranger-arc-2-0-2-august-18-2022"} title={"Cell Ranger ARC 2.0.2 (August 18, 2022)"}>

- Bug fixes

  - Fixes a bug where an upgrade to Illumina NovaSeq control software v1.8 (reagent name change in recipe XML file) resulted in a silent cellranger-arc mkfastq error and a significant number of reads going into Undetermined/ because the orientation of i5 (Index2) could not be autodetected

</LinkableSection>

<LinkableSection id={"cell-ranger-arc-2-0-1-february-3-2022"} title={"Cell Ranger ARC 2.0.1 (February 3, 2022)"}>

- Bug fixes

  - Fixes an issue where the metric "post-normalization number of reads" in the `aggr` web summary was incorrect.
  - Fixes an issue where integer overflow could occur on large `aggr` or `reanalyze` runs.
  - Fixes an issue where sample indices in the FASTQ header line were ignored unless the indices were reverse complemented.
  - Fixes an issue where gex_umis_count in per_barcode_metrics.csv were all zeros.

</LinkableSection>

<LinkableSection id={"cell-ranger-arc-2-0-may-3-2021"} title={"Cell Ranger ARC 2.0 (May 3, 2021)"}>

- New [wavelet-based peak caller](/support/software/cell-ranger-arc/latest/algorithms-overview/algorithms-overview#atac-matrix-computer):

  - Eliminates large peaks much larger than 5kb. Peaks have a tighter size distribution around ~ 1kb.
  - Improves detection of cluster-specific peaks.
  - Improves reproducibility between technical replicates.
  - Consistent performance across a range of cell loads.
  - Fixes crashes in the signal-background fitting procedure.

- Changed the duplicate marking algorithm:

  - Two read pairs are duplicates if they share the same start, end and cell barcode. Previously, only the start and end were used.
  - Boosts median fragments per cell by as much as 25% at high cell loads.
  - PCR and sequencer duplicates are no longer distinguished.

- Improved computational performance:

  - Up to 4x faster, 0.5x disk requirements.
  - Complete rewrite of read processing and differential accessibility analysis in Rust.
  - Minimize disk I/O.

- Added the `aggr` pipeline to [aggregate multiple libraries from multiple GEM wells](/support/software/cell-ranger-arc/latest/analysis/aggregating-multiple-gem-wells-aggr).
- Added the `reanalyze` pipeline to enable [customized reanalysis](/support/software/cell-ranger-arc/latest/analysis/customized-secondary-analysis-reanalyze).
- Changed cell caller override: when `--min-atac-count=X` and `--min-gex-count=Y` is specified we choose all barcodes with atac count >= X **and** (previously **or**) gex count >= Y.
- The raw feature barcode matrix now only contains barcodes with at least one ATAC count or one GEX count; previously, all allowed barcodes were present.
- Change in barcode error correction: correct Hamming distance 1 errors (previously 2).
- Added header lines beginning with `#` to the fragments.tsv.gz and peaks.bed files that contain version, reference and sample information.
- Change to ATAC peak annotation TSV format:

  - The `peak` column is now split into three columns: `chrom`, `start`, `end`.
  - When a peak has multiple gene annotations, the same peak appears in multiple rows with each annotation. Previously, each row represented one peak and multiple annotations were expressed using `;` separators in the same row.

- Improvements to reference construction:

  - Restrictions on the number of contigs or gene-containing contigs (primary contigs) in the reference have been eliminated.
  - Bug fix for GTFs that do not contain a `gene_name` attribute.
  - Contig names are allowed to contain `-` or `_` characters.
  - Eliminated discrepancies between reference checks in `mkref` and preflight checks in `count`. Previously, it was possible to pass checks in `mkref` and fail checks in `count`.

- Eliminated secondary alignments from the position-sorted BAM.
- Loupe browser files generated by the pipeline can only be opened by Loupe browser version 5.0 or later.

</LinkableSection>

<LinkableSection id={"cell-ranger-arc-1-0-1-december-10-2020"} title={"Cell Ranger ARC 1.0.1 (December 10, 2020)"}>

- Increases the upper limit on primary contigs (those that have at least one gene annotation) from 100 to 500. The pipeline will error out if more than 1000 total contigs are present in the reference.
- Disables multithreading in mkref to address an issue where mkref would fail on hardware without AVX support. This will be fixed in a future release.

</LinkableSection>

<LinkableSection id={"cell-ranger-arc-1-0-0-september-9-2020"} title={"Cell Ranger ARC 1.0.0 (September 9, 2020)"}>

- Creates `cellranger-arc count` for the analysis of 10x Chromium Single Cell Multiome ATAC + Gene Expression data generated from a single GEM well.
- Creates `cellranger-arc mkfastq` for demultiplexing of ATAC or GEX flow cell data for analysis.
- Creates `cellranger-arc mkref` to construct reference packages for use with `cellranger-arc count` starting with a reference FASTA file and a gene annotations GTF file.
- Note: the software cannot be used for the analysis of 10x Chromium Single Cell ATAC, 10x Chromium Single Cell 3' Gene Expression data, or for any kind of joint analysis of the two.

</LinkableSection>


Release Notes for Cell Ranger ARC

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

Downloads & Installation

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

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

Analyzing GEX + ATAC (count)

Aggregating Multiple Samples (aggr)

Custom Analysis (reanalyze)

Learn more about the output files generated by Cell Ranger

Outputs

Web Summary

ATAC + Gene Expression Analysis

Feature-Barcode Matrices

Per Barcode Metrics

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

What is Cell Ranger ARC?

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.