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bio-hi-c-analysis-contact-pairs

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Process Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data. Use when processing raw Hi-C read pairs.

When to use

• Process raw Hi-C read pairs
• Parse aligned Hi-C reads into contact pairs
• Filter duplicates
• Classify pair types (cis/trans)
• Generate contact statistics
• Filter by pair type
• Filter by distance
• Filter by MAPQ

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