HiCdat: a fast and easy-to-use Hi-C data analysis tool.
BACKGROUND
The 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.


RESULTS
HiCdat 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).


CONCLUSIONS
HiCdat 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.
Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, Zürich, 8008, Switzerland. marcschmid@gmx.ch.|Zurich-Basel Plant Science Center, Universitätstrasse 2, Zürich, 8092, Switzerland. marcschmid@gmx.ch.
Marc W
MW
Schmid
Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, Zürich, 8008, Switzerland. sgrob@botinst.uzh.ch.|Zurich-Basel Plant Science Center, Universitätstrasse 2, Zürich, 8092, Switzerland. sgrob@botinst.uzh.ch.
Stefan
S
Grob
Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, Zürich, 8008, Switzerland. grossnik@botinst.uzh.ch.|Zurich-Basel Plant Science Center, Universitätstrasse 2, Zürich, 8092, Switzerland. grossnik@botinst.uzh.ch.
Ueli
U
Grossniklaus
D002875:Chromosomes; D023281:Genomics / Q000379:methods*; D006801:Humans; D012313:RNA / Q000235:genetics*; D012984:Software; D013223:Statistics as Topic
D012313:RNA