Basic4Cseq

Basic4Cseq analyzes 4C-seq (Circular Chromosome Conformation Capture sequencing) data to process, filter, and visualize near-cis chromatin interactions for studies of genome architecture and gene regulation.

Key Features:

• Data Processing: Processes aligned 4C-seq raw data in BAM format and maps short reads to virtual fragment libraries.
• Virtual Fragment Libraries: Creates virtual fragment libraries compatible with any BSGenome package, annotating chromosome position, fragment length, uniqueness of fragment ends, and blindness status.
• Filtering Functions: Provides an optional BAM filter to remove invalid reads and functions to filter 4C-seq fragments based on predefined criteria.
• Quality Control: Implements basic quality control measures that assess read distribution across fragments.
• Visualization Tools: Generates coverage plots using a running median approach and multi-scale contact profiles for fragment data near the viewpoint.
• Data Export Options: Exports processed fragment data into Wig and CSV formats.

Scientific Applications:

• Gene regulation studies: Characterizes chromatin interactions relevant to transcriptional regulation.
• Enhancer–promoter interaction analysis: Identifies and visualizes enhancer-promoter contacts in cis.
• Three-dimensional genome architecture: Profiles near-cis contact patterns to inform studies of genome organization.
• Near-cis chromatin interaction profiling: Maps and quantifies interactions proximal to a specific viewpoint.

Methodology:

Processes BAM-aligned 4C-seq reads by mapping them to virtual fragment libraries constructed from BSGenome packages, applies optional BAM and fragment-level filters, assesses read distribution for quality control, and produces coverage plots using a running median and multi-scale contact profiles with output export to Wig or CSV.