Protocol for generating customizable and reproducible plots of sequencing coverage data using the seqNdisplayR package

Søren Lykke-Andersen; Jérôme O Rouvière; Manfred Schmid; Maria Gockert; Torben Heick Jensen

doi:10.1016/j.xpro.2024.102960

Protocol for generating customizable and reproducible plots of sequencing coverage data using the seqNdisplayR package

STAR Protoc. 2024 Mar 18;5(2):102960. doi: 10.1016/j.xpro.2024.102960. Online ahead of print.

Authors

Søren Lykke-Andersen¹, Jérôme O Rouvière², Manfred Schmid², Maria Gockert², Torben Heick Jensen³

Affiliations

¹ Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark. Electronic address: sla@mbg.au.dk.
² Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark.
³ Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark. Electronic address: thj@mbg.au.dk.

Abstract

The widespread usage of next-generation sequencing methods for functional genomics studies requires standardized tools for consistent visualization of the associated data. Here, we present seqNdisplayR, an R package for plotting standard sequencing data coverage within a genomic region of interest in a customizable and reproducible manner. We describe steps for installing software, preparing data files, choosing options, and plotting data. This tool is readily available for users with no prior experience with R through the "Shiny app" interface. For complete details on the use and execution of this protocol, please refer to Lykke-Andersen et al.,¹ Gockert et al.,² and Rouviere et al.³.

Keywords: ChIP; ChIP-seq; Chromatin immunoprecipitation; Gene Expression; RNA-seq; Sequencing.