Chromium Single Cell ATAC
Cell Ranger ATAC2.1, printed on 02/21/2024
Cell Ranger ATAC 2.1 (April 4, 2022)
- New features:
- Added a batch correction algorithm to
cellranger-atac aggr, intended for use when aggregating datasets that use different chemistries. See the aggr and algorithms pages for more details on how and when to use batch effect correction.
- Added UMAP as an alternate projection in Loupe and Cell Ranger ATAC output files.
- Added support for custom peaks with peaks on non-primary contigs.
- Minor cell calling improvements:
- Added less stringent filtering of low-targeting barcodes.
- Improved calling on multi-species samples.
- Reference changes:
- Added support for overlapping gene annotations in cellranger-atac mkref.
- Cell Ranger ATAC 2.1 can only be run on references generated by cellranger-atac mkref version 2.1 or 2.0. Cell Ranger ATAC 2.0 can only be run on references that are constructed using cellranger-atac mkref version 2.0.
- Web summary improvements:
- Enabled improved identification of the non-nucleosomal fragment fraction. The metric "fragments in nucleosome free regions" reported in the web_summary.html has been redefined as the fraction of high quality fragments smaller than 124 basepairs (previously, the threshold was 147 basepairs).
- Increased warning threshold for number of called cells from 10k to 15k.
- Added warning to web summary when forcing cell calls to unsupported levels.
- Added notification when user is using custom peaks or forcing cell calls.
- Added links to support pages.
- Bug fixes:
- Added missing format version (
VN:) to header of BAM file.
- Removed dependence on external Unix commands in BAM processing.
- The metric "Fraction of fragments overlapping any targeted region" reported in the web_summary.html was dropped in version 2.0 because some custom reference lacks DNase HS sites, or promoter/enhancer data, but the metric was still present in the aggr web_summary.html. This empty metric has been removed in version 2.1.
Cell Ranger ATAC 2.0 (May 3, 2021)
New wavelet-based peak
- Eliminates large peaks much larger than 5kb. Peaks have a tighter size
distribution around ~ 1kb.
- Improved detection of cluster-specific peaks.
- Improved reproducibility between technical replicates.
- Consistent performance across a range of cell loads.
- Fixes crashes in the signal-background fitting procedure.
Change in 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.
- We no longer distinguish between PCR and sequencer duplicates.
Improved computational performance:
- Up to 4x faster, 0.5x disk requirements.
- Complete rewrite of read processing and differential accessibility analysis
- Minimize disk I/O.
Change to pre-built references:
- The following additional annotation tracks have been removed:
- As a consequence, columns in the
singlecell.csv output for the
corresponding tracks are all zero. Additionally, the
column, which is a sum of TSS, DNAse, enhancer and promoter columns
represents the TSS fragments. This value would be lower than expected for
Breaking changes to reference package structure:
- Cell Ranger ATAC 2.0 pipelines cannot be run with a version 1.2 reference.
Cell Ranger ARC 1.0+ or Cell Ranger ATAC 2.0 references must be used.
- Restrictions on the number of contigs or primary contigs in the reference
have been eliminated.
- Change to the config file format to construct a reference using
- Primary contigs are now defined to be the set of gene-containing contigs and
cannot be specified by the user.
- Disabled support for URLs in the config file.
- Disabled support for GFF annotations, annotations must be in GTF format.
- Eliminated discrepancies between reference checks in
mkref and preflight
count. Previously, it was possible to pass checks in
fail checks in
Added header lines beginning with
# to the fragments.tsv.gz and peaks.bed
files that contain version, reference and sample information.
--downsample option and replaced by
Change to ATAC peak annotation:
- Annotate peaks using all genes provided in the reference GTF. Previously
only certain gene types were used for annotation.
peak column is now split into three columns:
- 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.
Change to CSV definition file format for
cellranger-atac aggr: eliminated
peaks column. Custom peaks may be specified using a
--peaks argument at
the command line.
Eliminated normalization mode
Loupe browser files now contain pre-computed K-means clustering for K=2-5
Loupe browser files generated by the pipeline can only be opened by Loupe
browser version 5.0 or later.
The web_summary.html file output from
cellranger-atac count has been updated
to be functionally consistent with that from
The PLSA algorithm is restricted to use one thread and computational
performance is likely to be affected.
Change to metric names in summary.csv generated by
Eliminated secondary alignments from the position-sorted BAM.
Cell Ranger ATAC 1.2.0 (November 21, 2019)
Cell Ranger ATAC v1.2 now filters gel bead multiplets and barcode multiplets, leading to more accurate cell calling. For customers concerned about either of these issues, we would recommend running Cell Ranger ATAC v1.2.
- Allow robust handling of GFF3 input in
- Fix a bug in the pre-generated human references where the Human
Pseudoautosomal Region (PAR) genes are filtered out.
- Fix a bug in reporting the erroneous line number of mal-formatted bed file
containing comment header lines.
- Fix a bug where the adjusted fragment bounds exceed the size of contig to
which the fragment is mapped.
- Fix a bug in peak calling where the initialization of the mixture model
fitting involved integer division instead of floating point division.
- Fix an issue in the peak calling algorithm where the mixture components were
not always ordered with respect to each other in the same consistent way,
leading to occasional stringent peak calls.
- Fix a bug in the interpolation formula used to evaluate the sensitivity of the
assay at various downsampled depths.
- Allow better handling of whitespaces in file paths in
- Add new metrics to metrics.json: median unique fragments per cell overlapping
peaks, percentage of genome in peaks, barcode and gel bead multiplet rate.
- Fix a bug in the web summary file where the alert color for cell calls is not
consistent with the thresholds.
- Add a feature to the websummary where a guidance message is printed at the top
of the html file.
- Mask out barcodes associated with gel bead doublets from the set of barcodes
on which cell calling is performed.
- Mask out barcodes associated with barcode multiplets from the set of barcodes
on which cell calling is performed.
Cell Ranger ATAC 1.1.0 (April 17, 2019)
- Include new
mkref tool to allow building of single-species custom references
from fasta and gene annotations.
- Remove metrics related to targeting based on custom files that may not be
available for custom genomes.
- Include new
reanalyze pipeline to allow rerunning data from a finished
pipeline but with custom selection of peaks and barcodes, along with tweaking
- Include new
aggr pipeline to allow aggregating data from multiple pipelines
and analyzing it as one dataset.
- Include GC and depth normalized differential enrichment analysis for
accessibility of transcription factor binding motifs.
- Include depth normalized differential enrichment analysis for accessibility in
- Improve peak annotation to include associations of genes with distal peaks.
- Improve performance of motif scanning by setting moderate background
nucleotide frequencies for peaks in extreme GC bins.
- Analysis output directory now has
enrichment in place of
- Fix an issue in peak calling where signal and noise components of a mixture
model get swapped and produces nonsensical threshold. Fixes via changing the
mixture model components.
- Fix an issue in peak calling where odds-ratio determines the wrong threshold
that would lead to calling entire genome in peaks.
- Replace the default clustering for LSA and PLSA based dimensionality
reductions to be
spherical k-means in place of
- Add an additional step to filter out low targeting barcodes prior to cell
calling, for better cell calling.
- Update references to include transcripts.bed file derived from gene
annotations, used in annotating peaks.
Cell Ranger ATAC 1.0.1 (December 17, 2018)
- Fix an issue in which some peak annotations were reversed.
- Update references to fix an off-by-one issue in some tss.bed entries.
- Fix an issue where PLSA would crash on CPUs without AVX support.
- Fix a division-by-zero issue in calculating the background nucleotide % during
Cell Ranger ATAC 1.0.0 (October 29, 2018)