Abstract
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.
| Original language | American English |
|---|---|
| Title of host publication | Methods in Molecular Biology |
| Pages | 45-54 |
| Number of pages | 10 |
| DOIs | |
| State | Published - Oct 23 2021 |
| Externally published | Yes |
Publication series
| Name | Methods in Molecular Biology |
|---|---|
| Volume | 2391 |
Bibliographical note
Publisher Copyright:© 2022, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Funding
This work is supported by the USDA National Institute of Food and Agriculture, Hatch project FLA-FTL-005926. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the National Institute of Food and Agriculture (NIFA) or the US Department of Agriculture (USDA).
| Funders | Funder number |
|---|---|
| U.S. Department of Agriculture | |
| National Institute of Food and Agriculture | FLA-FTL-005926 |
ASJC Scopus Subject Areas
- Molecular Biology
- Genetics
Keywords
- DESeq2
- Data analysis
- Differentially expressed genes
- HISAT2
- Pipeline
- RNA-seq
- Splice-aware
- StringTie
- Transcript profile
- Transcriptome
Disciplines
- Biology
- Life Sciences