---
title: "02-dge"
format: html
editor: visual
---

# Downloading reference genome
```{bash}
cd data
curl --insecure -O https://gannet.fish.washington.edu/seashell/bu-github/nb-2023/Cgigas/data/rna.fna
```
Downloading reference genome to the data folder. 

```{bash}
/home/shared/kallisto/kallisto \
index -i \
data/cgigas_roslin_rna.index \
data/rna.fna
```
Renaming and indexing rna.fna.

# Downloading sequence reads
```{bash}
cd data
wget --recursive --no-parent --no-directories \
--no-check-certificate \
--accept '*.fastq.gz' \
https://gannet.fish.washington.edu/seashell/bu-github/nb-2023/Cgigas/data/nopp/
```

...the rest of the workflow continues in 02-RNAseq.qmd. 