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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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

Yong-Hwee Eddie Loh¹, Li Shen^2,3

¹Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Methods in Molecular Biology (Clifton, N.J.)

|April 27, 2016

Summary

This summary is machine-generated.

ngs.plot is a bioinformatics tool that visualizes next-generation sequencing (NGS) data. It helps researchers analyze spatial relationships in genomic data and generate publication-ready figures efficiently.

Keywords:

ChIP-seq Heatmap RNA-seq Visualization ngs.plot

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Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

Next-generation sequencing (NGS) technologies generate vast amounts of data requiring efficient analysis.
Extracting novel biological insights from complex genomic datasets remains a challenge.

Purpose of the Study:

To introduce ngs.plot, a user-friendly bioinformatics tool for visualizing NGS data.
To enable customizable analysis of spatial relationships between sequencing enrichment and genomic features.

Main Methods:

Developed ngs.plot, a bioinformatics tool for data visualization.
Utilized command-line executions and a Galaxy-based web workflow for demonstration.
Applied ngs.plot to a previously published biological dataset.

Main Results:

ngs.plot effectively visualizes spatial relationships in NGS data.
The tool allows for analysis of user-defined genomic regions beyond standard databases.
Publication-ready figures were generated, demonstrating the tool's utility.

Conclusions:

ngs.plot provides an efficient and innovative method for mining NGS datasets.
Users can analyze their data without deep technical expertise in sequence coverage or databases.
The tool facilitates the generation of high-quality figures for scientific publications.