03-fastqc_multiqc.Rmd

---
title: "fastqc and multiqc"
output: html_document
date: "2023-11-15"
---

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

### FastQC to evaluate the quality of our sequence data

Self to do notes: - download the software (dowload the win/linux zip file for command line access) or find file path for Raven -

```{bash}

#making a directory for our fastqc output to be saved to, within our more general 'output' directory
mkdir ../output/fastQC-output/

```

```{bash}

/home/shared/FastQC-0.12.1/fastqc ../data/raw/*fastq.gz -o ../output/fastQC-output/
```

check output folder contents

```{bash}

ls ../output/fastQC-output/

```

# MultiQC

move to fastqc directory

```{bash}

eval "$(/opt/anaconda/anaconda3/bin/conda shell.bash hook)"
conda activate
which multiqc 

cd ../output/fastQC-output
pwd

multiqc .

```