Difference between revisions of "FastQC"

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[[Category:Software]][[Category:Biology]][[Category:NGS]]
 
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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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==Required Modules==
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==Environment Modules==
[[Modules|modules documentation]]
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
*{{#var:app}}
 
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
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See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
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=Validation=
 
* Validated 4/5/2018
 

Latest revision as of 15:25, 15 August 2022

Description

fastqc website  

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.

Environment Modules

Run module spider fastqc to find out what environment modules are available for this application.

System Variables

  • HPC_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/.