Chromosight benchmarks and processed data
Description
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.
Files
Files
(2.4 GB)
Name | Size | Download all |
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md5:7daf25490681ce9e32f55f343c263d00
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317.9 MB | Download |
md5:3d00efc58a14bff3d3a92355a5a0de79
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2.0 GB | Download |
md5:a0531a13642e9234ef5bc2efb2e83ecf
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119.6 MB | Download |
Additional details
Related works
- Is supplement to
- Preprint: 10.1101/2020.03.08.981910 (DOI)