---
title: "Gene annotation"
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
)
```

## Summary
Here I will try to annotate the Manila clam genes. I know NCBI has annoation and I will also blast to SP to get GO information.


# What does NCBI have?

![](http://gannet.fish.washington.edu/seashell/snaps/2024-08-30_13-59-11.png)
<https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_026571515.1/>


Grabbing the code clicking on 'datasets' button in screenshot

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

/home/shared/datasets \
download genome accession GCF_026571515.1 --include gff3,rna,cds,protein,genome,seq-report
```

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

```

```{r, engine='bash', eval = TRUE}
head /home/shared/8TB_HDD_03/sr320/github/clamgonads-macsamples/data/ncbi_dataset/data/GCF_026571515.1/*
```