Challenge #1 

Visualizing Overlapping Data Between Replicate Experiments


We perform experiments in the lab that isolate regions of the genome that are interesting in some way. In particular, one assay (Next Generation Capture-C) reports on evidence of physical interactions between one specific region of the genome with all other possible locations. The output of these experiments is a BED file that contains genomic intervals or coordinates.
In order to increase our confidence in the output of the experiment and identify real signal from background noise, we run each experiment multiple times generating a BED file for each replicate. We are interested in visualizing the intervals of the genome where there is a high degree of overlap between the identified contacts within these BED files.
Given a set of BED files, produce and visualize data that characterizes the amount of supporting evidence (number of overlapping intervals) for all locations. Bonus points will be given if the solution is able to accept the amount of overlap as input (e.g. user defines how much overlap they require: more than 1 base of overlap or even allow for negative overlap with a specified distance).

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2019 HudsonAlpha Tech Challenge

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