Abstract
BackgroundChromatin conformation capture techniques have evolved rapidly over the last few years and have provided new insights into genome organization at an unprecedented resolution. Analysis of Hi-C data is complex and computationally intensive involving multiple tasks and requiring robust quality assessment. This has led to the development of several tools and methods for processing Hi-C data. However, most of the existing tools do not cover all aspects of the analysis and only offer few quality assessment options. Additionally, availability of a multitude of tools makes scientists wonder how these tools and associated parameters can be optimally used, and how potential discrepancies can be interpreted and resolved. Most importantly, investigators need to be ensured that slight changes in parameters and/or methods do not affect the conclusions of their studies.ResultsTo address these issues (compare, explore and reproduce), we introduce HiC-bench, a configurable computational platform for comprehensive and reproducible analysis of Hi-C sequencing data. HiC-bench performs all common Hi-C analysis tasks, such as alignment, filtering, contact matrix generation and normalization, identification of topological domains, scoring and annotation of specific interactions using both published tools and our own. We have also embedded various tasks that perform quality assessment and visualization. HiC-bench is implemented as a data flow platform with an emphasis on analysis reproducibility. Additionally, the user can readily perform parameter exploration and comparison of different tools in a combinatorial manner that takes into account all desired parameter settings in each pipeline task. This unique feature facilitates the design and execution of complex benchmark studies that may involve combinations of multiple tool/parameter choices in each step of the analysis. To demonstrate the usefulness of our platform, we performed a comprehensive benchmark of existing and new TAD callers exploring different matrix correction methods, parameter settings and sequencing depths. Users can extend our pipeline by adding more tools as they become available.ConclusionsHiC-bench consists an easy-to-use and extensible platform for comprehensive analysis of Hi-C datasets. We expect that it will facilitate current analyses and help scientists formulate and test new hypotheses in the field of three-dimensional genome organization.
Highlights
Chromatin conformation capture techniques have evolved rapidly over the last few years and have provided new insights into genome organization at an unprecedented resolution
Some focus on matrix correction, others on detection of specific chromatin interactions and their differences across conditions and others on visualization of these interactions
Very few of these tools offer a complete Hi-C analysis (e.g., HiC-Pro), addressing tasks which range from alignment to interaction annotation
Summary
We used HiC-bench to analyze several published Hi-C datasets and the results of our analysis are presented below. We performed a comprehensive analysis calculating the TAD boundary overlaps for biological replicates of the same sample (as described in Methods section), using different TAD callers and different main parameter values for each TAD caller (Fig. 3a). In addition to the increase in the mean value of boundary overlap upon correction, we observed that the standard deviation of boundary overlaps among replicates decreased (again, with the exception of DI) (Fig. 3c) While this seems to be the trend for almost all TAD caller/parameter value combinations, the effect of correction in variance is more profound in certain cases (e.g., hicintra-max) than others.
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