bedtools-genomic-intervals

To calculate read depth and coverage breadth over specified genomic intervals, use coverage analysis operations on coordinate-sorted BAM or BED files. This Skill processes these formats to output precise per-base and region coverage metrics for genomic intervals.

To identify the closest genomic features to a given set of intervals, use nearest neighbor identification operations. This Skill processes coordinate-sorted interval files to output the nearest features, useful for annotating peaks by distance to Transcription Start Sites.

Yes, coordinate-sorted input is required for most genomic interval operations. Additionally, a genome file is necessary for certain manipulations like interval complementing, ensuring accurate genome arithmetic when processing BED, BAM, GFF, and VCF files.

The best way to annotate ChIP-seq peaks with overlapping genes is by using interval intersection and nearest feature annotation. This Skill identifies overlapping genes and calculates distances to the nearest Transcription Start Site for comprehensive peak annotation.