Version Compatibility

Reference examples tested with: cooler 0.9+, pairtools 1.1+, pandas 2.2+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Hi-C Contact Pairs Processing

"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 Workflow Overview