coral-embryo-RNAseq

This repository contains code and output for a gene expression analysis of coral embryos exposed to 3 increasing levels of polyvinyl chloride (PVC) leachate. Montipora capitata rice coral embryos were subjected to a single-stressor ecotoxicology assay designed to test the impact of PVC leachate on their early development. You can check out the complimentary repositories for a development coral-embryo-scope and microbiome (coral-embryo-microbiome) coral-embryo-microbiome analysis from the same ecotoxicological assay.

RNA-seq Analysis Pipeline

flowchart TD
    A[Raw RNA-seq Data] --> B[Quality Control]
    B --> C[Read Alignment]
    C --> D[Transcript Quantification]
    D --> E[Differential Expression Analysis]
    E --> F[Functional Enrichment]
    F --> G[Visualization & Reporting]

    subgraph Preprocessing
        A
        B
    end

    subgraph Analysis
        C
        D
        E
        F
    end

    subgraph Output
        G
    end

Loading

The bioinformatics pipeline includes:

• Quality Control: FastQC and Fastp for filtering and trimming reads
• Read Alignment: HISAT2 for mapping reads to reference genome
• Transcript Quantification: Counting gene/transcript abundances
• Differential Expression Analysis: DESeq2 for identifying significant expression changes
• Functional Enrichment: GO enrichment using goseq
• Visualization & Reporting: Generating plots and reports using rrvgo and ggplot2