MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites - PubMed (original) (raw)
MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites
Anthony O Olarerin-George et al. Bioinformatics. 2017.
Abstract
Summary: An increasing number of studies are mapping protein binding and nucleotide modifications sites throughout the transcriptome. Often, these sites cluster in certain regions of the transcript, giving clues to their function. Hence, it is informative to summarize where in the transcript these sites occur. A metagene is a simple and effective tool for visualizing the distribution of sites along a simplified transcript model. In this work, we introduce MetaPlotR, a Perl/R pipeline for creating metagene plots.
Availability and implementation: The code and associated tutorial are available at https://github.com/olarerin/metaPlotR .
Contact: srj2003@med.cornell.edu.
© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com
Figures
Fig. 1.
Metagene of m6A sites. This metagene of N-6 methyladenosine sites (m6A) was generated with MetaPlotR. The metagene shows the characteristic peak in RNA methylation around the CDS end/3′UTR start. The metagene also highlights an optional feature of MetaPlotR—re-scaling of the 5′UTR, CDS and 3′UTR plotted lengths to reflect the average size of these regions in the queried dataset
References
- Dominissini D. et al. (2012) Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature, 485, 201–206. - PubMed
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