---
title: "01-data-wrangling"
author: "Zach Bengtsson"
date: "2023-04-13"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

Get data from reef genomics genome assembly (GFF3) and scaffolds (FASTA)...
```{bash genome download}
wget -P /home/shared/8TB_HDD_02/zbengt/github/zach-lncRNA/data http://pver.reefgenomics.org/download/Pver_genome_assembly_v1.0.gff3.gz
gunzip /home/shared/8TB_HDD_02/zbengt/github/zach-lncRNA/data/Pver_genome_assembly_v1.0.gff3.gz
wget -P /home/shared/8TB_HDD_02/zbengt/github/zach-lncRNA/data http://pver.reefgenomics.org/download/Pver_genome_assembly_v1.0.fasta.gz
gunzip /home/shared/8TB_HDD_02/zbengt/github/zach-lncRNA/data/Pver_genome_assembly_v1.0.fasta.gz
```

Download the RNA-seq data from gannet. This downloads all of it, only working with 1 for now...
```{bash rna-seq data}
wget -r \
--no-check-certificate \
--quiet \
--no-directories --no-parent \
-P /home/shared/8TB_HDD_02/zbengt/data/zach-lncRNA/data \
-A *fastq.gz \
https://gannet.fish.washington.edu/Atumefaciens/hputnam-Becker_E5/Becker_RNASeq/data/raw/
```

Grabbing the P ver gtf Sam created...
```{bash gtf}
curl -o ../data/Pver_genome_assembly_v1.0-valid.gtf https://gannet.fish.washington.edu/Atumefaciens/20230127-pver-gff_to_gtf/Pver_genome_assembly_v1.0-valid.gtf
```