Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot

The continual maturation and increasing applications of next-generation sequencing technology in scientific research have yielded ever-increasing amounts of data that need to be effectively and efficiently analyzed and innovatively mined for new biological insights.

Researchers at the Icahn School of Medicine have developed ngs.plot-a quick and easy-to-use bioinformatics tool that performs visualizations of the spatial relationships between sequencing alignment enrichment and specific genomic features or regions. More importantly, ngs.plot is customizable beyond the use of standard genomic feature databases to allow the analysis and visualization of user-specified regions of interest generated by the user’s own hypotheses.

In this protocol, the researchers demonstrate and explain the use of ngs.plot using command line executions, as well as a web-based workflow on the Galaxy framework. They replicate the underlying commands used in the analysis of a true biological dataset that we had reported and published earlier and demonstrate how ngs.plot can easily generate publication-ready figures. With ngs.plot, users are able to efficiently and innovatively mine their own datasets without having to be involved in the technical aspects of sequence coverage calculations and genomic databases.


Screenshot of ngs.plot interface on Galaxy

Availability – ngsplot is avialble at:

Loh YH, Shen L,. (2016) Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot. Methods Mol Biol 1415:371-83. [abstract]

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