Recipes

This section provides practical examples and patterns for common genomic analysis tasks using GIQL. Each recipe focuses on a specific use case with ready-to-use query patterns.

Recipe Categories

Intersection

Finding overlapping features, filtering by overlap, counting overlaps, strand-specific operations, and join patterns.

Distance and Neighbors

Calculating distances between features, finding nearest neighbors, distance-constrained searches, and directional queries.

Clustering and Merging

Clustering overlapping intervals, distance-based clustering, merging intervals, and aggregating cluster statistics.

Advanced Queries

Multi-range matching, complex filtering with joins, aggregate statistics, window expansions, and multi-table queries.

Coming from Bedtools?

If you’re familiar with bedtools and want to replicate specific commands in GIQL, see the Bedtools Migration Guide guide for a complete mapping of bedtools operations to GIQL equivalents.