Chapter Title

RNA-seq Data Analysis for Differential Expression

Book Title

Methods in Molecular Biology

Authors

Navdeep Gill, University of Arkansas, Fayetteville
Braham Dhillon, University of Florida

Files

Document Type

Book Chapter

Editors

John M. Walker

Description

Changes in the surrounding environment are mirrored by changes in the transcript profile of an organism. In the case of a plant pathogen, host colonization would be a challenge that triggers changes in transcript expression patterns. Determining the transcriptional profile could provide valuable clues on how an organism responds to defined stimuli, in this case, how a pathogen colonizes its host. Several robust data analysis methods and pipelines are available that can identify these differentially expressed transcripts. In this chapter we outline the steps and other caveats that are needed to run one such pipeline.

ISBN

978-1-0716-1795-3

Publication Date

10-23-2021

Publisher

Springer

Keywords

RNA-seq, Transcriptome, Transcript profile, Data analysis, Pipeline, Differentially expressed genes, Splice-aware, HISAT2, StringTie, DESeq2

Disciplines

Biology | Life Sciences

NSUWorks Citation

Gill, Navdeep and Braham Dhillon. (2021). RNA-seq Data Analysis for Differential Expression. In John M. Walker (Eds.), Methods in Molecular Biology (45-54).

ORCID ID

0000-0003-3746-1866

DOI

10.1007/978-1-0716-1795-3_4