This script merges the locations of loops detected at several resolutions.

Loops in the inputFiles need to have the following format:

chr start end chr start end

Loops are merged if the x and y position of a loop overlap with the x and y position of another loop; all loops are considered as an overlap within +/- the bin size of the lowest resolution. I.e. for a loop with coordinates x and y, the overlap with all other loops is checked for (x - lowest resolution) and (y + lowest resolution). If two or more locations are to be merged, the loop at the lowest resolution is taken as the merged loop.

Example usage:

$ hicMergeLoops -i gm12878_10kb.bedgraph gm12878_5kb.bedgraph gm12878_25kb.bedgraph -o merged_result.bedgraph -r 25000

Please recall: We work with binned data i.e. the lowest resolution is therefore the one where we merge the most bases into one bin. In the above example the lowest resultion is 25kb, the highest resolution is 5kb.

usage: hicMergeLoops --inputFiles INPUTFILES [INPUTFILES ...] --outFileName
                     OUTFILENAME --lowestResolution LOWESTRESOLUTION [--help]

Required arguments

--inputFiles, -i

The loop files from hicDetectLoops. To use files from other sources, please follow ‘chr start end chr start end’ format and remove any header.

--outFileName, -o

The name of the merged loop file.

--lowestResolution, -r

The lowest resolution of all loop files, i.e. 5kb, 10kb and 25kb, please use 25000.

Optional arguments


show program’s version number and exit