---
title: "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
---

```{r setup, include=FALSE}
library(knitr)
library(tidyverse)
library(kableExtra)
library(DESeq2)
library(pheatmap)
library(RColorBrewer)
library(data.table)
library(DT)
library(formattable)
library(Biostrings)
library(spaa)
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
)
```


Running kallisto 

trimmed files are at https://gsafjobs.icmb.utexas.edu/tagseq_prep/JA22078_SA22060/fq.trim/A1-T001F_S100_L099_R1_cmb.trim.fastq.gz

```{bash}
wget -r \
--no-directories --no-parent \
--password JA22078 \
-P ../data \
-A "*.fastq.gz" https://gsafjobs.icmb.utexas.edu/tagseq_prep/JA22078_SA22060/fq.trim/
```