---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2018-09-10 19:33:39+00:00
layout: post
slug: sequencing-data-analysis-c-virginica-oil-spill-mbdseq-concatenation-fastqc
title: Sequencing Data Analysis - C.virginica Oil Spill MBDseq Concatenation & FastQC
categories:
  - 2018
  - LSU C.virginica Oil Spill MBD BS Sequencing
tags:
  - FASTQC
  - jupyter notebook
  - multiqc
  - roadrunner
  - Xserve
---

Per [Steven's request](https://github.com/RobertsLab/resources/issues/366), I concatenated our _Crassostrea virginica_ LSU oil spill MBDseq sequencing data and ran FastQC on the concatenated files.

Here's the list of input files:

`2112_lane1_ACAGTG_L001_R1_001.fastq.gz
2112_lane1_ACAGTG_L001_R1_002.fastq.gz
2112_lane1_ATCACG_L001_R1_001.fastq.gz
2112_lane1_ATCACG_L001_R1_002.fastq.gz
2112_lane1_ATCACG_L001_R1_003.fastq.gz
2112_lane1_CAGATC_L001_R1_001.fastq.gz
2112_lane1_CAGATC_L001_R1_002.fastq.gz
2112_lane1_CAGATC_L001_R1_003.fastq.gz
2112_lane1_GCCAAT_L001_R1_001.fastq.gz
2112_lane1_GCCAAT_L001_R1_002.fastq.gz
2112_lane1_TGACCA_L001_R1_001.fastq.gz
2112_lane1_TTAGGC_L001_R1_001.fastq.gz
2112_lane1_TTAGGC_L001_R1_002.fastq.gz`

All commands were run on roadrunner (Apple Xserve; Ubuntu 16.04). See Jupyter notebook below for details.

Jupyter notebook (GitHub):





  * [20180910_roadrunner_virginica_fastqc.ipynb](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20180910_roadrunner_virginica_fastqc.ipynb)





* * *





# RESULTS:



The concatenated gzip files and FastQC/MultiQC files are in the output folder linked below.

Output folder:





  * [20180910_Cvirginica_oil_fastqc/](https://owl.fish.washington.edu/Athaliana/20180910_Cvirginica_oil_fastqc/)



MultiQC report (HTML):



  * [20180910_Cvirginica_oil_fastqc/multiqc_report.html](https://owl.fish.washington.edu/Athaliana/20180910_Cvirginica_oil_fastqc/multiqc_report.html)