---
title: "week01"
format: html
editor: visual
---

## downloading files to raven from klone

The first set of 16 files comprise 8 individual samples from Grays Harbor, Washington (W*.fastq.gz), each with two files representing both DNA read directions.

```{bash}
cd ../data
rsync --archive --progress --verbose lbreit@klone.hyak.uw.edu:/gscratch/scrubbed/lbreit/fish546/W*.fastq.gz .
```

The second set of 16 files comprise 8 individual samples from Padilla Bay, Washington (P*.fastq.gz), each with two files representing both DNA read directions.

```{bash}
cd ../data
rsync --archive --progress --verbose lbreit@klone.hyak.uw.edu:/gscratch/scrubbed/lbreit/fish546/P*.fastq.gz .
```

Next, I will use the FastQC program for quality control...

...first I need to create an output file.
```{bash}
pwd
#mkdir ../output
```
```{bash}
# run fastqc
/home/shared/FastQC-0.12.1/fastqc -t 36 -o ../output ../data/*.fastq.gz

```

# MultiQC

...scans all subdirectories and files within this path for QC reports (e.g., FastQC outputs) and aggregates them into a single HTML report. This report provides visualizations and summaries of QC metrics across multiple samples

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

cd ../output/
multiqc .
```
woohoo!!!

# Interpretation 

to follow...
