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Day 4: Sequencing QC

Day 4: Sequencing QC

Welcome to Day 4 of the Short-Read Sequencing Analysis Workshop. After Day 4 you should have a basic understanding of how to use FastQC to evaluate the quality of your short-read data and how to trim your reads using Trimmomatic. We will also be reviewing barcoding/indexing and some of the considerations to using barcodes for multiplex sequencing.

Videos for Day 4

**Please note all videos are from 2015

Video1: Barcoding (7:38)  This video will go over many of the design considerations for barcoding/indexing, as well as the demultiplexing process 

Video2: Post-sequencing quality evaluation (22:52)  This video will explain the fastq file format, review some of the sources of library read quality problems and introduce you to the FastQC program. In addition it will explain how to troubleshoot various problems using the FastQC program output. 

Video3: Running FastQC (11:31)  This video will walk through an example of read quality evaluation with FastQC

Video4: Running Trimmomatic (15:35)  This video will introduce you to the Trimmomatic program that can be used to trim reads for adapter contamination or low quality bases. 


Day 4 files

In-class slides for Day 4

Cheat sheet for Day 4

Day 4 Homework 

Day 4 Homework PBS script - The edited PBS script to run Trimmomatic and FastQC on the homework set

FastQC output files: Day4HW_R1.fastqDay4HW_R2.fastqDay4HW_R1_paired_out.fastqDay4HW_R2_paired_out.fastq  **Note that the file names in the FastQC output are different, the names were changed for ease of use.


Additional resources

FastQC website 

Another FastQC video

FastQC manual (pdf file)

Trimmomatic website

Trimmomatic manual (pdf file)

Trimmomatic paper (pdf file)

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