Pairs

Pairs stores paired genomic coordinates in a block-compressed text format and enables indexed querying to support analysis of Hi-C and other paired-end chromatin interaction datasets.

Key Features:

• Block-Compressed Text File Format: Pairs uses block-compression to store paired genomic coordinates, reducing storage for large Hi-C datasets while preserving fast retrieval.
• Pairix: Indexing and Querying Application: Pairix, implemented in C with additional implementations in Python and R, extends Tabix to index and query paired coordinates, enabling rapid access to specific genomic interactions.
• PairsQC: Quality Control Reporting: PairsQC generates collapsible HTML-based quality control reports for Pairs-format Hi-C datasets to assess data integrity.

Scientific Applications:

• Chromatin Architecture Analysis: Enables exploration of 3D chromosome organization and genome folding effects on gene regulation using Hi-C read pairs.
• Epigenetic Studies: Facilitates investigations of how chromosomal interactions correlate with epigenetic modifications.
• Comparative Genomics: Supports comparative analyses across species or cell types by efficient management of large interaction datasets.

Methodology:

Block-compression of paired coordinates and indexing via Pairix (an extension of Tabix) provide compact storage and fast queries, and PairsQC produces collapsible HTML quality-control reports.