Biology Faculty Books and Book Chapters
RNA-seq Data Analysis for Differential Expression
Book Title
Methods in Molecular Biology
ORCID ID
0000-0003-3746-1866
Document Type
Book Chapter
ISBN
978-1-0716-1795-3
Publication Date
10-23-2021
Editors
John M. Walker
Keywords
RNA-seq, Transcriptome, Transcript profile, Data analysis, Pipeline, Differentially expressed genes, Splice-aware, HISAT2, StringTie, DESeq2
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.
DOI
10.1007/978-1-0716-1795-3_4
Publisher
Springer
First Page
45
Last Page
54
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 .