This pipeline includes scripts I generated to analyze transcriptomes for differential expression with samples from C. gigas and C. virginica.
For each species they perfom the following analysis
- Adapter trimming, quality trimming using BBTools
- Mapping with HISAT2 to the reference genome
- Alignment with Stringtie to the reference annotation
- Differential Transcript analysis of count data with DESeq2
The following script is only available for C. gigas transcriptomes.
- Gene set enrichment analysis (GSEA) with topGO
The /SCRIPTS folder contains bash scripts to be executed from a cluster computing environment. The /Bac_Viral_Subset folder contains scripts to process C. gigas transcriptomes. The /C_Virginica_Subset folder contains scripts to process C. virginica transcriptomes.
The DESeq2 folder contains R scripts to perform DESeq2 differential transcript analysis and GSEA (Gene Set Enrichment Analysis). Scripts again are separated into separate folders by species.
Adidtionally, I have provided a folder called "Streamlined Pipeline Tutorial" where I provide a Markdown file with resources for where to find each tool, step by step instructions of how to use the pipeline, and rationale for how I set up the pipeline. I also include relevant papers as well as a powerpoint providing an introduction to reference-based RNA-seq in general.
To cite this work: Roberts, E.M. 2020. "Pipeline to perform differential expression analysis with transcriptomes". https://github.com/erinroberts/apoptosis_data_pipeline. The University of Rhode Island.