10x Genomics
Single Cell ATAC
Cell Ranger ATAC, printed on 09/18/2024
Release Notes for 1.2
Cell Ranger ATAC 1.2.0 (2019-11-21)
|
|
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.
