---
title: "01-Data-Explore"
format: html
editor: visual
---

# Having a look at my methylation data

1. Get data onto raven to start exploring !!

This gets all fastq.gz files at given url and puts in data directory...
```{bash}
cd ../data 
wget --recursive --no-parent --no-directories \
--no-check-certificate \
--accept '*.fastq.gz' \
http://owl.fish.washington.edu/nightingales/M_trossulus/
```


# Lets Ignore!

MAKE sure you ignore BEFORE you STAGE... Otherwise it will index large files that takes forever.

```{bash}
cd ../data
echo '*.fastq.gz' >> .gitignore
sort -u .gitignore -o .gitignore
```

# md5

```{bash}
ls ../data/*.gz | xargs -n 1 -P 24 md5sum > ../output/01-Data-Explore/md5sums.txt
```



# run fastqc ...

```{bash}
/home/shared/FastQC-0.12.1/fastqc -t 36 -o ../output/01-Data-Explore ../data/*.fastq.gz
```


# have a pretty look with multiQC..

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

cd ../output/01-Data-Explore/
multiqc .
```
