for July 2024 Montipora capitata

Using the table of annotated differentially expressed genes **(generated in step 5)**, make some insightful data visualizations to understand the differing key biological processes between coral embryos and coral recruits

Using the table of annotated differentially expressed genes **(generated in step 5)**, make some insightful data visualizations to understand the differing key biological processes between coral embryos and coral recruits

Merge the table of differentially expressed genes **(generated with `DESeq2` in step 3)** to the table of annotated genes **(generated using `Blast`in step 4)** to explore the functions of the differentially expressed genes

A Differential Gene Expression analysis of *Montipora capitata* corals from two life-history stages [](https://zenodo.org/badge/latestdoi/621460253)

Use `UniProt` (a protein sequence and gene-ontology (GO) functional information database) and `BLAST` (a sequence search algorithm) to annotate the **Montipora capitata** reference genome

Use `curl` and `wget` to pull sequence data from NCBI and a reference genome from Rutgers University

Use a count matrix generated in Step 2 as input to `DESeq2` to generate a negative binomial model and output a list of significantly differentially expressed genes

Create a gene expression count matrix from `kallisto` output files

Using the table of annotated differentially expressed genes **(generated in step 5)**, make some insightful data visualizations to understand the key biological processes that the differentially expressed genes are involved in

Using DESeq2 to make a list of differentially expressed genes from the negative binomial distribution

A snapshot in time of learning about differential gene expression analysis and making lots of mistakes

creating an index file from Montipora capitata annotated genome V3

Code for taking RNA-seq data, and running a common differential gene expression analysis, without the use of a reference genome. The end product will be a number of plots and table of differentially expressed genes.

Lesson plan for FISH441/541A Thursday May 26, 2022