Nucleosome positioning software tools | MNase sequencing data analysis
Nucleosomes consisting of approximately 146 base pairs (bp) of DNA wrapped around a histone octamer are the fundamental structural units of chromatin in metazoans. The translational positioning of nucleosomes along DNA is implicated in profoundly influencing gene expression. Thus, defining the nucleosome positioning and occupancy is critical to understand the mechanisms of regulation of transcription by chromatin.
A package for non-parametric nucleosome positioning. nucleR uses a novel aproach in this field which comprises a deep profile cleaning using Fourier Transform and peak scoring for a quick and flexible nucleosome calling.
A bioinformatic tool that generates nucleosome occupation maps from chromatin digestion with micrococcal nuclease (MNase-seq), chemical cleavage (CC-seq), chromatin inmunoprecipitation (ChIP-seq) and fragmentation by sonication. This wavelet-based tool requires only two inputs: the dataset of aligned short reads and the sequence of the reference genome.
Analyzes deep sequencing data for chromatin maps. TemplateFilter identifies nucleosome positions from Illumina sequencing data and automatically extracts nucleosome position, occupancy, and width, and accounts for variability in end digestion by MNase. The method is based on identifying occupancy templates of forward and reverse reads that are typical of nucleosomes.
Allows users to plot the 2D occupancy (2DO) of genomic data. plot2DO allows the investigation of paired-end sequencing data originating from a variety of organisms. It assists user in creation of 2D occupancy plots permitting researchers to determine quality of micrococcal nuclease sequence (MNase-seq) data. This tool is useful for visualization of the distribution of nucleosomes near the functional regions of the genome.
Addresses both the positional heterogeneity across cells and experimental biases by seeking nucleosomes consistently positioned in a cell population and showing a significant enrichment relative to a control sample. Despite the absence of validated dataset, NucleoFinder (i) detects fewer false positives than two other nucleosome calling methods and (ii) identifies two important features of the nucleosome organization (the nucleosome spacing downstream of active promoters and the enrichment/depletion of GC/AT dinucleotides at the centre of in vitro nucleosomes) with equal or greater ability than the other two methods.
An R package designed for processing aligned reads from chromatin-oriented high-throughput sequencing experiments. Pasha allows easy manipulation of aligned reads from short-read sequencing technologies (ChIP-seq, FAIRE-seq, MNase-seq...) and offers innovative approaches such as ChIP-seq reads elongation, nucleosome midpoint piling strategy for positioning analyses, or the ability to subset paired-end reads by groups of insert size that can contain biologically relevant information. It integrates several options allowing a seamless adaptation to various experimental setups. Additionally, the R package provides several tools for programmers that need to develop or integrate additional features.
A command line tool for accurate placing of the nucleosomes. NOrMAL was designed to resolve overlapping nucleosomes and extract extra information ("fuzziness", probability, etc.) of nucleosome placement.