1-iv. Pre-Alignment QC

You can use FastQC to get a sense of your data quality before alignment:

• http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Video Tutorial here:

• http://www.youtube.com/watch?v=bz93ReOv87Y

Make an output directory, run FastQC on a fastq file, and view the outputs in Firefox:

    cd $RNAWORKING
    mkdir fastqc
    fastqc $RNARAW/HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz -outdir fastqc/
    firefox fastqc/HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1_fastqc.html

Another useful QC program is SolexaQA++ (which can also do various trimming steps).

• http://solexaqa.sourceforge.net/

To obtain help on the program and a list of options on the command-line, enter:

# SolexaQA++ and subprograms help
SolexaQA++

SolexaQA++ analysis

SolexaQA++ dynamictrim

SolexaQA++ lengthsort

# Fastqc help
fastqc --help

Make an output directory, run SolexaQA++ on a fastq file, and view some PDF outputs in a file browser window:

    mkdir solexaqa
    SolexaQA++ analysis $RNARAW/HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz -d solexaqa
    gnome-open solexaqa

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PRACTICAL EXERCISE 3

Assignment: Run FASTQC or SolexaQA++ on one of the additional fastq files.

• Hint: Remember that this data is stored as read-only compressed files in $RNARAW.
• Hint: Both FASTQC and SolexaQA++ can run on compressed (.gz) files.
• Hint: To get help on using these programs, try

    SolexaQA++ help
    fastqc -help

• Hint: You can also simply run:

   fastqc

This will pop up the GUI (Graphical User Interface) version of fastqc. In the GUI, you can select any files, run fastqc and view the report.

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