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BI
bio-hi-c-analysis-contact-pairs
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-hi-c-analysis-contact-pairs
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: pairtools parse → pairtools sort → pairtools dedup → pairtools stats.
- Process my Hi-C read pairs" → Parse aligned Hi-C reads into contact pairs, filter duplicates, classify pair types (cis/trans), and generate contact statistics. CLI: pairtools parse → pairtools sort → pairtools dedup → pairtools stats.
- Process Hi-C read pairs with pairtools.
- pairtools parse \ --chroms-path chromsizes.txt \ --min-mapq 30 \ --walks-policy 5unique \ --output parsed.pairs.gz \ aligned.bam.
Source Doc
Excerpt From SKILL.md
With restriction enzyme cut sites
pairtools parse
--chroms-path chromsizes.txt
--min-mapq 30
--walks-policy 5unique
--add-columns mapq
aligned.bam |
pairtools restrict -f enzyme_sites.bed |
gzip > parsed.restricted.pairs.gz
## Sort pairs by position
pairtools sort \
--nproc 8 \
--output sorted.pairs.gz \
parsed.pairs.gz
Mark and remove PCR duplicates
pairtools dedup
--max-mismatch 1
--mark-dups
--output deduped.pairs.gz
--output-stats dedup_stats.txt
sorted.pairs.gz
Use cases
- Use when processing raw Hi-C read pairs.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- hic-data-io - Work with cooler matrices
- matrix-operations - Balance resulting matrices
- read-alignment - Align Hi-C reads before processing
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