At the moment, running an aggregate command of a whole signal track against a complete peak dataset takes a considerable amount of time; the equivalent action using bedtools (bigWigToBedGraph -> bedtools map) is about 10x faster (give or take depending on I/O load). Potential speed ups might rely on parallel processing (1 process per chromosome; bedtools is not parallelized, though).
felipealbrecht
commented
8 years ago
At the moment, running an aggregate command of a whole signal track against a complete peak dataset takes a considerable amount of time; the equivalent action using bedtools (bigWigToBedGraph -> bedtools map) is about 10x faster (give or take depending on I/O load). Potential speed ups might rely on parallel processing (1 process per chromosome; bedtools is not parallelized, though).