Genomic intervals & annotation / Flanks and promoters
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“Promoter” locates the TSS by strand (start for +, end for −) and extends the chosen lengths upstream and downstream. Upstream 2000 with downstream 0 gives “2 kb upstream of the TSS”, a common promoter definition for promoter or peak analyses.
“Flanks” take only the sequence outside the interval. When strand-aware, “left” means upstream (on the right for − strand); lengths can be a fraction of the interval length (rounded down).
Regions are clipped at 0 and, with a length file, at the chromosome end; zero-length flanks are dropped. Other columns (name, score, strand) are kept as they are.
The output can go straight into the other interval tools (intersect, coverage, closest).
Flank rules match BEDTools flank (-l/-r/-b/-s/-pct); promoters equal a strand-aware slop of the 1 bp TSS (Quinlan & Hall 2010, Bioinformatics 26:841); both checked line by line on the same inputs.
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