Differential Enriched Scan 2 (DEScan2): a fast pipeline for broad peak analysis
- Published
- Accepted
- Subject Areas
- Bioinformatics, Genomics
- Keywords
- epigenomics, bioinformatics, atac-seq, peak calling, pipeline
- Copyright
- © 2018 Righelli et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2018. Differential Enriched Scan 2 (DEScan2): a fast pipeline for broad peak analysis. PeerJ Preprints 6:e27357v1 https://doi.org/10.7287/peerj.preprints.27357v1
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.
Author Comment
This is an abstract which has been accepted for the BBCC2018 Conference