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Dataset Open Access

Chromosight benchmarks and processed data

Matthey-Doret, Cyril; Montagne, Rémi; Baudry, Lyam; Cournac, Axel

Input data and scripts required to rerun chromosight's benchmarks and associated figures, as well as output results in text format.

The record contains 2 tarballs corresponding to two different benchmarks. Each tarball contains the scripts, input and output data of its benchmark:

Performance benchmark:

This benchmark is contained in "20200406_benchmark_chromosight_performance.tar.gz" and compares chromosight running time and RAM use with 2 other softwares. This benchmark is run on a real high resolution human Hi-C matrix with different subsampling values. Benchmark scripts are expected to be run on a regular laptop or desktop.

Results benchmark:

This benchmark is contained in "20200406_benchmark_chromosight_results.tar.gz" and assess chromosight's ability to detect chromatin loop patterns on Hi-C contact maps. Chromosight is compared to 4 other softwares. For each software, precision, recall (=sensitivity) and F1 scores are measured using 2000 small synthetic Hi-C matrices with known loop coordinates. Each software is run with a range of 50-200 parameter combinations for all data. Scripts to run this benchmark are written to run as a job array on a SLURM computing cluster to reduce compute time.

Processed data files

The contact matrices in cool format, which are used to generate figures throughout the manuscript.

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