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Contact Pairs Processing - Usage Guide

Overview

This skill covers processing Hi-C read pairs using pairtools, including parsing, sorting, deduplication, and filtering to generate valid contact pairs.

Prerequisites

conda install -c bioconda pairtools cooler

Quick Start

Tell your AI agent what you want to do:

  • "Process my Hi-C BAM file with pairtools"
  • "Filter valid pairs from my pairs file"

Example Prompts

Basic Processing

"Parse Hi-C pairs from this BAM"

"Remove duplicates from my pairs file"

Filtering

"Select only UU pair types"

"Remove self-ligation artifacts"

Statistics

"Get statistics from my pairs file"

"How many valid pairs do I have?"

What the Agent Will Do

  1. Parse alignments to pairs format
  2. Sort pairs by position
  3. Remove PCR duplicates
  4. Filter by pair type
  5. Generate statistics

Tips

  • Pair types - UU (unique-unique) are highest confidence
  • MAPQ - Filter for MAPQ >= 30 for quality
  • Self-ligation - Remove pairs < 1kb apart
  • Pipeline - Use pipes to chain operations