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Related Concept Videos

RNA-seq03:21

RNA-seq

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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...
9.9K

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RNA-Seq Data Analysis for Differential Gene Expression Using HISAT2-StringTie-Ballgown Pipeline.

Vivek Thakur1

  • 1Department of Systems & Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India. vivek22@uohyd.ac.in.

Methods in Molecular Biology (Clifton, N.J.)
|July 27, 2024
PubMed
Summary

This study provides a guide for routine RNA-sequencing (RNA-seq) analysis using whole genome sequences. It helps biologists discover candidate genes and understand biological mechanisms, especially for new users.

Keywords:
BallgownDifferential gene expressionHISAT2Mapping to whole genome referencePlant datasetRSEMStringTieTranscript abundance

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Comparative transcriptome analysis is a key tool for identifying candidate genes in biological research.
  • While lacking the resolution of genetic studies, transcriptome comparisons offer valuable insights into biological processes.
  • Advancements in sequencing technologies have increased the utility of transcriptome analysis.

Purpose of the Study:

  • To provide a protocol for first-time users to conduct routine RNA-sequencing (RNA-seq) analysis.
  • To guide researchers in utilizing whole genome sequences as a reference for RNA-seq data analysis.
  • To facilitate candidate gene discovery and understanding of biological mechanisms through RNA-seq.

Main Methods:

  • The study outlines a protocol for standard RNA-sequencing data analysis.
  • It emphasizes the use of whole genome sequences as a reference dataset.
  • The protocol is designed for users new to RNA-seq analysis.

Main Results:

  • A clear, step-by-step protocol for conducting routine RNA-seq analysis is presented.
  • The guide facilitates the use of whole genome references for accurate analysis.
  • The protocol aims to simplify the process for novice researchers.

Conclusions:

  • This protocol serves as a valuable resource for biologists new to RNA-seq analysis.
  • It enables efficient candidate gene discovery and exploration of biological mechanisms.
  • The availability of this guide promotes wider adoption of RNA-seq in research.