w4CSeq

w4CSeq analyzes 4C-Seq (Circularized Chromosome Conformation Capture followed by deep sequencing) data to identify genome-wide interacting partners of specified loci and quantify enrichment of genomic features around 4C sites while supporting both enzyme digestion and sonication fragmentation-based protocols.

Key Features:

• Data Input Flexibility: Accepts raw 4C sequencing data in FASTQ format.
• Protocol Support: Supports enzyme digestion and sonication fragmentation-based 4C methodologies.
• Automated Statistical Analysis: Automates statistical analysis of 4C-Seq data to detect significant interactions.
• Interaction Detection: Identifies genome-wide partners interacting with specific loci and outputs lists of candidate interacting genomic sites and regions.
• Visualization Capabilities: Generates figures illustrating genome-wide distribution of interacting regions and visualizes enrichment of transcription start sites (TSSs), transcription termination sites (TTSs), CpG islands, and DNA replication timing near 4C sites.

Scientific Applications:

• Chromatin interaction mapping: Mapping genome-wide contacts of specified loci to study chromatin architecture and spatial genome organization.
• Regulatory network analysis: Identifying distal interacting regions and their enrichment for genomic features to inform regulatory networks that influence gene expression and cellular function.

Methodology:

Processes raw FASTQ 4C-Seq reads, performs automated statistical analysis to identify interacting regions, and produces lists and figures summarizing genome-wide distributions and enrichment of TSSs, TTSs, CpG islands, and DNA replication timing.