---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2018-05-16 22:00:13+00:00
layout: post
slug: fastqc-rrbs-geoduck-bs-seq-fastq-data
title: FastQC - RRBS Geoduck BS-seq FASTQ data
categories:
  - 2018
  - Miscellaneous
tags:
  - FASTQC
  - geoduck
  - jupyter notebook
  - multiqc
  - Panopea generosa
  - roadrunner
  - RRBS
---

[Earlier today I finished trimming](https://robertslab.github.io/sams-notebook/posts/2018/2018-05-16-trimgalorefastqcmultiqc-trimgalore-rrbs-geoduck-bs-seq-fastq-data/) Hollie's RRBS BS-seq FastQ data.

However, the original files were never analyzed with FastQC, so I ran it on the original files.

These libraries were originally created by Hollie Putnam using the TruSeq DNA Methylation Kit (Illumina):





  * [project_juvenile_geoduck_OA/Sample_Processing (GitHub)(https://github.com/hputnam/project_juvenile_geoduck_OA/tree/master/Sample_Processing)



FastQC was run, followed by MultiQC. Analysis was run on Roadrunner.

All analysis is documented in a Jupyter Notebook; see link below.



###### Jupyter Notebook:







  * [20180516_roadrunner_geoduck_EPI_fastqc](https://github.com/sr320/LabDocs/blob/master/jupyter_nbs/sam/20180516_roadrunner_geoduck_EPI_fastqc.ipynb)





* * *





##### Results:





###### FastQC output folder:







  * [20180516_geoduck_EPI_fastqc/](https://owl.fish.washington.edu/Athaliana/20180516_geoduck_EPI_fastqc/)





###### MultiQC output folder:







  * [20180516_geoduck_EPI_fastqc/multiqc_data](https://owl.fish.washington.edu/Athaliana/20180516_geoduck_EPI_fastqc/multiqc_data)





###### MultiQC report (HTML):







  * [multiqc_report.html](https://owl.fish.washington.edu/Athaliana/20180516_geoduck_EPI_fastqc/multiqc_data/multiqc_report.html)