thesis-RNAseq

Analysis of B. saida full transcriptome data from raw reads to gene ontology

Steps outlined in this repository:

1. Demultiplexing
2. QA/QC
3. Adapter trimming with Bbduk
4. Genome indexing and alignment with STAR
5. Feature count with htseq-count
6. Verification of sample inter-comparability
7. Differential gene expression (DGE) analysis
   • identification of up and downregulated genes with DESeq2
   • conversion of genes to standardized UIDs with NCBI's eFetch Utility
   • annotation of biological processes and assignment of gene ontologies using FishEnrichr
   • visualization of GO pathways using simplifyEnrichment

Steps 1-5 can be found in the pipeline, while inter-comparability verification is carried out in R (version 4.0.3 (2020-10-10)) through the approach described in fish stats and DGE is documented in the DESeq2 markdown. For additional reading, including a deeper discussion of these analyses, check out my MSc. thesis.