Difference between revisions of "FastQC"
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| + | Note that FastQC 0.11 changes how duplication is calculated as described in [http://proteo.me.uk/2013/09/a-new-way-to-look-at-duplication-in-fastqc-v0-11/ http://proteo.me.uk/2013/09/a-new-way-to-look-at-duplication-in-fastqc-v0-11/]. | ||
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Revision as of 17:58, 12 September 2014
Description
FastQC is an application which takes a FastQ file and runs a series of tests on it to generate a comprehensive QC report to tell if there is anything unusual about your sequence. Each test is flagged as a pass, warning or fail depending on how far it departs from what you'd expect from a normal large dataset with no significant biases. It's important to stress that warnings or even failures do not necessarily mean that there is a problem with your data, only that it is unusual. It is possible that the biological nature of your sample means that you would expect this particular bias in your results.
Required Modules
Serial
- fastqc
System Variables
- HPC_{{#uppercase:fastqc}}_DIR - installation directory
How To Run
Note that FastQC 0.11 changes how duplication is calculated as described in http://proteo.me.uk/2013/09/a-new-way-to-look-at-duplication-in-fastqc-v0-11/.