Difference between revisions of "FastQC"
Moskalenko (talk | contribs) m (Text replace - "<!--Run-->" to "==System Variables== * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory <!--Run--> ") |
|||
| (4 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]] | + | [[Category:Software]][[Category:Biology]][[Category:NGS]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|fastqc}} | |{{#vardefine:app|fastqc}} | ||
| Line 7: | Line 7: | ||
|{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice --> | |{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice --> | ||
|{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice --> | |{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice --> | ||
| − | |{{#vardefine:exe|}} <!--RUNNING --> | + | |{{#vardefine:exe|1}} <!--RUNNING --> |
|{{#vardefine:conf|}} <!--CONFIGS--> | |{{#vardefine:conf|}} <!--CONFIGS--> | ||
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
| Line 23: | Line 23: | ||
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. | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | |||
| − | < | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==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/ http://proteo.me.uk/2013/09/a-new-way-to-look-at-duplication-in-fastqc-v0-11/]. | ||
|}} | |}} | ||
<!--Configuration--> | <!--Configuration--> | ||
Latest revision as of 15:25, 15 August 2022
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.
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/.