1. Using FastQC to QC raw reads

In our intial QC of the raw fastq file we will be interested in gathering various metrics, such as the total number of reads, sequence length, or GC content. We will also want to summarise such things as base quality scores and make assessments of the contamination of the reads with adapter sequence.

For this (and the next couple of sessions) we will working at the command line. If you are unfamiliar with the command line and “bash” shell command language, there is nice basic cheat sheet with the most commonly used commands here:

https://icosbigdatacamp.github.io/2018-summer-camp/slides/BASH_Cheat_Sheet.pdf

FastQC is a quality control tool for high throughput sequence data that is maintained by the Babraham Institute. It is free to download and use. It runs a number QC analyses on sequencing data (in various formats, not just fastq) and summarises the results in a easy to read report.

The basic command to run FastQC is simply fastqc.

Access the help page to find the basic usage an other options:

fastqc --help

The Usage is:

    fastqc seqfile1 seqfile2 .. seqfileN

    fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam]
           [-c contaminant file] seqfile1 .. seqfileN

The simplest way to use it is just to type fastqc followed by all the sequence files that you wish to QC. It will then run through as many files as you provide generating a report for each one.

There are many additional options that you can provide to modify the behaviour of the programme. The most common one is -o output_directory. By default the report is written to the same directory as the fastqc file, however, if you would like to gather the QC in a different directory, you can specify this using the -o flag followed by the name of the directory, e.g:

fastqc -o QC fastq/my_fastq_file.fastq.gz

In this case the above command will generate a report for the file my_fastq_file.fastq.gz, which is in the folder fastq, and will have the report written into a directory called QC.

Note that the output directory must already exist, FastQC will not create it.

Exercise 1

    1. Check the location of the current directory using the command pwd
    2. If the current directory is not Course_Materials, then navigate to the Course_Materials directory using the cd (change directory) command:
cd ~/Course_Materials
    1. Use ls to list the contents of the directory. There should be directory called fastq
    2. Use ls to list the contents of the fastq directory:
ls fastq

You should see two fastq files called SRR7657883.sra_1.fastq.gz and SRR7657883.sra_1.fastq.gz. These are the files for read 1 and read 2 of one of the samples we will be working with (you can ignore the other fastq files for now).

  1. Run fastqc on one of the fastq files:
fastqc fastq/SRR7657883.sra_1.fastq.gz

This will write the QC report to the fastq directory.

  1. Open the html report in a browser and see if you can answer these questions:
    A) What is the read length?
    B) Does the quality score vary through the read length?
    C) How is the data’s quality?

Note: In practice you would actually end up running FastQC on both read 1 and read 2 of every sample. This would usually results in large number of reports. Rather than having to open and inspect each one individually, we would normally gather them all together into a single report using the program MultiQC. We will cover MultiQC in the later session “QC of alignment”. ——————————————————————-