10x Genomics
Chromium Single Cell ATAC
Cell Ranger ATAC2.0, printed on 11/13/2024
Release Notes
Cell Ranger ATAC 2.0 (May 3, 2021)
-
New wavelet-based peak
caller:
- 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
in Rust.
- Minimize disk I/O.
-
Change to pre-built references:
- The following additional annotation tracks have been removed:
blacklist.bed
dnase.bed
ctcf.bed
enhancer.bed
promoter.bed
- As a consequence, columns in the
singlecell.csv
output for the
corresponding tracks are all zero. Additionally, the on_target_fragments
column, which is a sum of TSS, DNAse, enhancer and promoter columns
represents the TSS fragments. This value would be lower than expected for
this reason.
-
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
mkref
.
- 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
checks in count
. Previously, it was possible to pass checks in mkref
and
fail checks in count
.
-
Added header lines beginning with #
to the fragments.tsv.gz and peaks.bed
files that contain version, reference and sample information.
-
Eliminated the --downsample
option and replaced by --subsample-rate
.
-
Change to ATAC peak annotation:
- Annotate peaks using all genes provided in the reference GTF. Previously
only certain gene types were used for annotation.
- 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.
-
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 signal
from cellranger-atac aggr
.
-
Loupe browser files now contain pre-computed K-means clustering for K=2-5
(previously K=2-10).
-
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 cellranger-arc count
.
-
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 cellranger-atac count
.
-
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
mkref
.
- 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
mkref
.
- 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
analysis parameters.
- 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
peaks.
- 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 diff_tf
.
- 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 k-medoids
.
- 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
motif scanning.
Cell Ranger ATAC 1.0.0 (October 29, 2018)