BAMscale

BAMscale quantifies and normalizes peak coverage from BAM files and produces scaled coverage tracks and numerical scores for analysis of next-generation sequencing (NGS) datasets.

Key Features:

• One-Step Processing: Performs one-step quantification and normalization of peak coverage directly from BAM files.
• Wide Applicability: Supports ChIP-seq, ATAC-seq, END-seq, OK-seq, NS-seq, scRepli-seq, and splice-aware RNA-seq.
• Efficient Data Handling: Processes large BAM datasets (up to ~100 Gb) in minutes.
• Output Formats: Generates raw and normalized peak scores in text format and scaled BigWig coverage tracks.
• Normalization Options: Provides multiple normalization options for peak quantification.
• Visualization Module: Includes a visualization module for on-demand quantitative peak comparisons.

Scientific Applications:

• Chromatin profiling (ChIP-seq): Quantitative comparison of protein–DNA binding peaks from ChIP-seq datasets.
• Chromatin accessibility (ATAC-seq): Assessment of chromatin accessibility via ATAC-seq peak coverage and normalization.
• DNA double-strand break mapping (END-seq): Mapping and quantification of DNA double-strand break sites using END-seq.
• DNA replication and strand-specific assays (OK-seq, NS-seq, scRepli-seq): Analysis of DNA replication features and strand-specific signals using OK-seq, NS-seq, and scRepli-seq.
• Splice-aware RNA-seq: Quantification of splice-aware RNA-seq coverage for expression and splicing analyses.

Methodology:

BAMscale directly processes BAM files to quantify and normalize identified peaks, offers multiple normalization options, outputs raw and normalized peak scores in text format and scaled BigWig coverage tracks, and provides a visualization module for quantitative peak comparisons.