RNA-seq Bioinformatics

Introduction to bioinformatics for RNA sequence analysis

Pre-alignment QC


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

Video Tutorial here:

Try to run FastQC on your fastq files:

    cd $RNA_HOME/data
    fastqc *.fastq.gz

Then, go to the following url in your browser:

Exercise: Investigate the source/explanation for over-represented sequences:


Assignment: Run FASTQC on one of the additional fastq files you downloaded in the previous practical exercise.

Run FASTQC on the file ‘hcc1395_normal_1.fastq.gz’ and answer these questions by examining the output.


Solution: When you are ready you can check your approach against the Solutions.

Run MultiQC on your fastqc reports to generate a single summary report across all samples/replicates.

    cd $RNA_HOME/data
    multiqc .