---
title: "22-Apul methylation"
author: Steven Roberts
date: "`r format(Sys.time(), '%d %B, %Y')`"  
output: 
  html_document:
    theme: readable
    highlight: zenburn
    toc: true
    toc_float: true
    number_sections: true
    code_folding: show
    code_download: true
---

```{r setup, include=FALSE}
library(knitr)
library(tidyverse)
knitr::opts_chunk$set(
  echo = TRUE,         # Display code chunks
  eval = FALSE,         # Evaluate code chunks
  warning = FALSE,     # Hide warnings
  message = FALSE,     # Hide messages
  fig.width = 6,       # Set plot width in inches
  fig.height = 4,      # Set plot height in inches
  fig.align = "center" # Align plots to the center
)
```


Methylation files at https://owl.fish.washington.edu/nightingales/E5-coral-deep-dive-expression/genohub2216545/

![](http://gannet.fish.washington.edu/seashell/snaps/2025-02-05_07-56-52.png)



```{bash}
wget -r \
--no-directories --no-parent \
-P ../data \
-A "423*.gz,427*.gz,439*.gz,467*.gz,413*.gz" \
https://owl.fish.washington.edu/nightingales/E5-coral-deep-dive-expression/genohub2216545/
```