---
title: "Untitled"
output: html_document
date: "2025-02-19"
---




```{bash}
wget -r \
--no-directories --no-parent \
-P ../data/wgbs-trim \
-A "*gz" https://gannet.fish.washington.edu/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/
```
```{bash}
# Directories and programs
bismark_dir="/programs/Bismark-0.21.0"
bowtie2_dir="/programs/bowtie2-2.3.4.1-linux-x86_64/"
genome_folder="../data/"

bismark_genome_preparation \
--verbose \
--parallel 2 \
../../data/
```


```{r}
```

