---
title: "02-alignment"
author: "Kathleen Durkin"
date: "2025-04-29"
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output: 
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---

I'll be performing alignment of WGBS reads to the *C. virginica* genome using `bismark`. Sam has already generated scripts for this purpose as part of the [`ceasmallr`](https://github.com/sr320/ceasmallr/tree/main_) project, but I'll be rerunning alignment for the `FISH 546` bioinformatics class (SP 2025).

Download trimmed reads
```{r, engine='bash', eval=FALSE}
# Run wget to retrieve FastQs and MD5 files
# Note: the --no-clobber command will skip re-downloading any files that are already present in the output directory
wget \
--directory-prefix ../data/trimmed-WGBS-reads \
--recursive \
--no-check-certificate \
--continue \
--cut-dirs 4 \
--no-host-directories \
--no-parent \
--quiet \
--no-clobber \
--accept="*.fq.gz,checksums.md5" https://gannet.fish.washington.edu/gitrepos/ceasmallr/output/00.00-trimming-fastp/

```


Download scripts files
```{r, engine='bash'}

```