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Pasha / Preprocessing of Aligned Sequences from HTS Analyses

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.


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.