Genomic intervals & annotation / BED intersect / subtract
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Two intervals overlap when they share at least one base. Coordinates follow the BED convention (0-based start, end not included), so book-ended intervals do not overlap.
“Pairs” lists each overlapping pair on its own row, showing which B each A falls in. “A with any overlap” and “A with no overlap” filter intervals in or outside a class of regions (genes, peaks, a block list). “Count” gives the number of B per A.
“Subtract” removes the bases of A covered by B and may split an interval into pieces; “drop any A that overlaps” removes the whole interval instead.
A minimum overlap of 0.5 means the overlap must cover at least half of A (or B); with “reciprocal” both sides must meet it. Strand matching only uses intervals with a + or − strand.
Download the table as CSV; the BED text below keeps every original column and can be pasted into the next tool.
Overlaps are found with a per-chromosome sorted interval index; output columns and hit order match BEDTools intersect / subtract (Quinlan & Hall 2010, Bioinformatics 26:841), checked line by line on the same inputs.
Runs in your browser; up to roughly 50 MB per file (a few hundred thousand intervals) is recommended.
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