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Differential Enriched Scan 2 (DEScan2): a fast pipeline for broad peak analysis

Year: 2018
Type: preprint
Abstract: Nowadays, the analysis of RNA-seq and BS-Seq can be considered well established, whereas the analysis of broad peaks data as Sono-Seq/ATAC-Seq and histone modification (HM) ChIP-Seq is still challenging. To fill the gap in existing methods, we present DEScan2 a novel bioconductor package [2] for the analysis of broad peaks data. The method consists of three main steps: 1) a peak caller, 2) peak filtering and alignment across replicates and 3) a method to efficiently compute a count matrix of the filtered peaks. Using an already published ATAC-Seq dataset for chromatin accessibility our method shows interesting results, also by comparing it with other well-known tools for this kind of data analysis.
DOI: 10.7287/peerj.preprints.27357v1
Authors: Dario Righelli, John Koberstein, Nancy Zhang, Claudia Angelini, Lucia Peixoto, Davide Risso
Institutions: University of Salerno, Istituto per le Applicazioni del Calcolo Mauro Picone, National Research Council, Oregon Health & Science University, University of Pennsylvania, Washington State University Spokane, University of Padua, Cornell University, Weill Cornell Medicine
Language: English
Open Access status: green
OpenAlex ID: W2906126710
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Cited by: 2
Related to: 10