BatMeth2 is an easy-use Bisulfite sequencing (BS-Seq) analysis pipeline tool, which can align BS reads with high accuracy while allowing for variable-length indels with respect to the reference genome. Additionally, BatMeth2 can calculate the methylation levels of individual loci, genomic regions or functional regions such as genes/transposable elements. Additional programs were also developed to provide methylation data annotation, visualization, and differentially methylated cytosine/region (DMC/DMR) detection. The whole package provides new tools and will benefit bisulfite data analysis. BatMeth2 improves DNA methylation calling, particularly for regions close to indels. It is an autorun package and easy to use. In addition, a DNA methylation visualization program and a differential analysis program are provided in BatMeth2.
ChromSDE: Inference of Spatial Organizations of Chromosomes Using Semi-definite Embedding Approach and Hi-C Data
For a long period of time, scientists studied genomes assuming they are linear. Recently, chromosome conformation capture (3C) based technologies, such as Hi-C, have been developed that provide the loci contact frequencies among loci pairs in a genome-wide scale. The technology unveiled that two far-apart loci can interact in the tested genome. It indicated that the tested genome forms a 3D chromsomal structure is to model the 3D chromosomal structure from the 3C-dervied data computationally. This paper presents a deterministic method called ChromSDE, which applies semi-definite programming techniques to find the best structure fitting the observed data and uses golden section search to find the correct parameter for converting the contact frequency to spatial distance. To the best of our knowledge, ChromSDE is the only method which can guarantee recovering the correct structure in the noise-free case. In addition, we prove that the parameter of conversion from contact frequency to spatial distance will change under different resolutions theoretically and empirically. Using simulation data and real Hi-C data, we show that ChromSDE is much more accurate and robust than existing methods. Finally, we demonstrate that interesting biological findings can be uncovered from our predicted 3D structure(Visit ChromSDE).
ChIA-PET Tool is a software package for automatic processing of ChIA-PET sequence data, including linker filtering, mapping tags to reference genomes, identifying protein binding sites and chromatin interactions, and displaying the results on a graphical genome browser(Visit ChIA-PET Tool).