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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  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.
This is an abstract which has been accepted for the BBCC2018 Conference