---
title: "01-methykit"
output: html_document
---

```{r load packages, echo=TRUE, message=FALSE, warning=FALSE}
library(methylKit)
library(tidyverse)
```

```{bash}
/opt/homebrew/bin/wget -r \
--no-check-certificate \
--quiet \
--no-directories --no-parent \
-P ../data/ \
-A "[0-9]*sorted.bam" \
https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/061021-big/
```

## Samples IDS
sample_ids_list <- list("0501", "0502", "0503", "3501", "3502", "3503", ----SUS
                        "5201", "5202", "5203", "5901", "5902", "5903")