---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: FastQC-MultiQC - Additional C.gigas WGBS Sequencing Data from Genewiz Received 20190501
date: '2019-05-01 13:03'
tags:
  - Crassostrea gigas
  - Genewiz
  - Pacific oyster
  - bisulfite
  - BSseq
  - whole genome
  - fastqc
  - multiqc
categories:
  - 2019
  - Miscellaneous
---
Earlier today, we [received the additional _G.gigas_ sequencing data from Genewiz](https://robertslab.github.io/sams-notebook/posts/2019/2019-05-01-Data-Received-Additional-C.gigas-Whole-Genome-Bisulfite-Sequencing-Data-from-Genewiz/). Wanted to run through FastQC again and get an updated report for each data set. Admittedly, it probably won't look much different from [the initial FastQC run on 20190415](https://robertslab.github.io/sams-notebook/2019/04/15/FastQC-WGBS-Sequencing-Data-from-Genewiz-Received-20190408/), due to the fact that the additional sequencing was simply appended to the previous data. Since FastQC examines a subset of the data in each file, I'd fully expect the FastQC report to look the same. However, we'll have a greater number of sequences in each file. This should, in turn, increase the number of reads retained after quality trimming.

Ran FastQC, followed by MultiQC on my computer (swoose).

Used this bash script:

- [20190501_cgig_fastqc_wgbs_roberto.sh](http://gannet.fish.washington.edu/Atumefaciens/20190501_cgig_fastqc_wgbs_roberto/20190501_cgig_fastqc_wgbs_roberto.sh)

---

# RESULTS

Output folder:

- [20190501_cgig_fastqc_wgbs_roberto](http://gannet.fish.washington.edu/Atumefaciens/20190501_cgig_fastqc_wgbs_roberto/)

MultiQC Report (HTML):

- [20190501_cgig_fastqc_wgbs_roberto/multiqc_report.html](http://gannet.fish.washington.edu/Atumefaciens/20190501_cgig_fastqc_wgbs_roberto/multiqc_report.html)


As predicted, the "Per Tile Sequence Quality" test still fails, but the additional reads should help make up for the sequence loss we might experience during quality trimming:

![Screencap of example FastQC Per Sequence Tile failure](https://github.com/RobertsLab/sams-notebook/raw/master/images/screencaps/20190501_fastqc_tile_fail.png)