HiCdat: a fast and easy-to-use Hi-C data analysis tool |
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Authors: | Marc W. Schmid Stefan Grob Ueli Grossniklaus |
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Affiliation: | .Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, Zürich, 8008 Switzerland ;.Zurich-Basel Plant Science Center, Universitätstrasse 2, Zürich, 8092 Switzerland |
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Abstract: | BackgroundThe study of nuclear architecture using Chromosome Conformation Capture (3C) technologies is a novel frontier in biology. With further reduction in sequencing costs, the potential of Hi-C in describing nuclear architecture as a phenotype is only about to unfold. To use Hi-C for phenotypic comparisons among different cell types, conditions, or genetic backgrounds, Hi-C data processing needs to be more accessible to biologists.ResultsHiCdat provides a simple graphical user interface for data pre-processing and a collection of higher-level data analysis tools implemented in R. Data pre-processing also supports a wide range of additional data types required for in-depth analysis of the Hi-C data (e.g. RNA-Seq, ChIP-Seq, and BS-Seq).ConclusionsHiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes, their correlation to genomic and epigenomic features, and on comparative studies. It uses simple input and output formats and can therefore easily be integrated into existing workflows or combined with alternative tools.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0678-x) contains supplementary material, which is available to authorized users. |
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Keywords: | Chromosome Conformation Capture (3C) Nuclear architecture Hi-C Data analysis Sample comparison Structural domains Correlation to (epi-)genome |
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