scATACpipe

scATACpipe performs end-to-end processing and analysis of single-cell ATAC-seq (scATAC-seq) data to profile chromatin accessibility and regulatory landscapes at single-cell resolution.

Key Features:

• End-to-end workflow: Integrates quality assessment, preprocessing, dimension reduction, clustering, peak calling, and differential accessibility inference.
• Preprocessing options: Supports 10x Genomics Cell Ranger ATAC, Chromap, and custom preprocessing scripts.
• scRNA-seq integration: Enables joint analysis with single-cell RNA sequencing (scRNA-seq) to infer transcription factor activity, footprinting, co-accessibility, and cell trajectory prediction.
• Downstream analysis with ArchR: Leverages the R package ArchR for extended downstream analyses across eukaryotic species with annotated reference genomes.
• Output and visualization files: Produces cluster-specific BAM, BED, and BigWig files and generates an HTML report summarizing analysis results.
• Nextflow modular pipeline: Implemented in Nextflow to provide a modular workflow structure for the specified computational steps.

Scientific Applications:

• Regulatory landscape profiling: Mapping chromatin accessibility to identify regulatory elements and their cell-type specificity.
• Cell-type identification and differentiation: Resolving heterogeneous cell populations and inferring cellular differentiation trajectories.
• Multi-omic integration: Linking chromatin accessibility with gene expression and transcription factor activity via integration with scRNA-seq.
• Disease and mechanism studies: Identifying differential accessibility and regulatory changes associated with disease mechanisms.

Methodology:

Implemented as a Nextflow pipeline that integrates 10x Genomics Cell Ranger ATAC, Chromap, and custom preprocessing scripts, and uses the R package ArchR to perform quality assessment, preprocessing, dimension reduction, clustering, peak calling, differential accessibility inference, transcription factor activity analysis, footprinting, co-accessibility, and cell trajectory prediction, and to generate cluster-specific BAM, BED, BigWig files and an HTML report.