10x Genomics
Single Cell ATAC

Cell Ranger ATAC, printed on 03/18/2025

Release Notes for 1.1

Cell Ranger ATAC 1.1.0 (2019-04-17)

• 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.