---
title: "09-Hisat"
author: "Steven Roberts"
date: "`r format(Sys.time(), '%d %B, %Y')`"  
output: 
  github_document:
    toc: true
    toc_depth: 3
    number_sections: true
    html_preview: true
  html_document:
    theme: readable
    highlight: zenburn
    toc: true
    toc_float: true
    number_sections: true
    code_folding: show
    code_download: true
editor_options: 
  markdown: 
    wrap: sentence
---

```{r setup, include=FALSE}
library(knitr)
library(tidyverse)
library(kableExtra)
library(DT)
library(Biostrings)
library(tm)
knitr::opts_chunk$set(
  echo = TRUE,         # Display code chunks
  eval = FALSE,         # Evaluate code chunks
  warning = FALSE,     # Hide warnings
  message = FALSE,     # Hide messages
  fig.width = 6,       # Set plot width in inches
  fig.height = 4,      # Set plot height in inches
  fig.align = "center", # Align plots to the center
  comment = ""         # Prevents appending '##' to beginning of lines in code output
)
```


# Reads

```{r, engine='bash', eval=TRUE}
ls /home/shared/8TB_HDD_02/shedurkin/project-cod-temperature/output/05-cod-RNAseq-trimming/trimmed-reads
```
Need to find treatment file...



# Genome

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_031168955.1/

![genome](http://gannet.fish.washington.edu/seashell/snaps/Monosnap_Gadus_macrocephalus_genome_assembly_ASM3116895v1_-_NCBI_-_NLM_2024-05-15_09-20-59.png)
```{r, engine='bash'}
cd ../data

/home/shared/datasets download genome accession GCF_031168955.1 --include gff3,gtf,rna,cds,protein,genome,seq-report
```


```{r, engine='bash'}
cd ../data 
unzip ncbi_dataset.zip
```



```{r, engine='bash', eval=TRUE}
ls /home/shared/8TB_HDD_03/sr320/github/project-cod-temperature/data/ncbi_dataset/data/GCF_031168955.1

```