---
title: "QA/QC"
output: md_document
date: "2023-04-14"
---
File 2 of 3.

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, eval = FALSE, warning = FALSE, message = FALSE)
```

Below I specify where the FastQC software is at and then run the command fastqc on all RNAseq files in the folder called raw with the extension .fastq using the wildcard '*'. The output will be an html report that can be viewed in a web browser.

```{r, engine='bash'}
cd ../raw
/home/shared/FastQC/fastqc *.fastq

```

To open the html files run. Currently, this does not work so ask someone or troubleshoot later.

```{r, engine='bash'}
cd raw
open *.html
```