ChIA-PET2

ChIA-PET2 processes ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag Sequencing) data to identify chromatin interactions and characterize three-dimensional genome organization.

Key Features:

• Versatile Data Handling: Supports analysis of various types of ChIA-PET data derived from different experimental protocols.
• Integrated Workflow: Performs linker trimming, read alignment, duplicate removal, peak calling, and chromatin loop calling within a single pipeline.
• Quality Control: Incorporates quality control checks at multiple stages of data processing to assess data integrity and processing accuracy.
• Allele-Specific Interaction Analysis: Uses phased genotype data to call allele-specific chromatin interactions.

Scientific Applications:

• Chromatin Interaction Mapping: Identifies long-range chromatin loops and contacts from ChIA-PET sequencing data.
• Three-Dimensional Genome Organization: Characterizes spatial genome architecture relevant to gene regulation.
• Gene Regulation and Transcriptional Networks: Links chromatin interactions to potential regulatory elements and transcriptional control.
• Allele-Specific Genomic Analysis: Detects allele-specific chromatin architecture using phased genotype information to study genetic variation and disease-associated variants.

Methodology:

Computational steps include linker trimming, read alignment, duplicate removal, peak calling, chromatin loop calling, quality control checks, and allele-specific interaction calling using phased genotype data.