Difference between revisions of "FastQC"
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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. | 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. | ||
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Revision as of 02:39, 10 August 2012
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.
Execution Environment and Modules
To use fastqc with the environment modules system at HPC the following commands are available:
Get module information for fastqc:
$module spider fastqc
Load the default application module:
$module load fastqc
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_FASTQC_DIR - directory where fastqc is located.