---
title: "RNA-seq analyis on clam gonad samples"
author: "Megan Ewing"
format: 
  html:
    toc: true
---

### Retrieving data from Gannet

-   waiting on file path link / info on how to access the reads

making a directory specifically for the raw files

```{bash}
mkdir ../data/raw/
```

```{bash}

# get raw data from gannet origin but only dowload ".fastq.gz" files within that online directory, and limit search to just that directory (no parent directories)
wget -A "*.fastq.gz" -r -np -nd -P ../data/raw/ "https://gannet.fish.washington.edu/mewing0/Man_clam_raw/" 

```

### Checking file integrity via MD5sums

```{bash}

md5sum --quiet -c ".../data/raw/" 

```