Difference between revisions of "STAR"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|star}} | |{{#vardefine:app|star}} | ||
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635 "STAR: ultrafast universal RNA-seq aligner" | A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635 "STAR: ultrafast universal RNA-seq aligner" | ||
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| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | Make sure to set a directory for temporary files within your /blue working directory with the '<code>--outTempDir</code> argument to avoid job crashes and filling up diskless compute nodes. See [[Temporary Directories]] for more information. | |
|}} | |}} | ||
<!--PBS scripts--> | <!--PBS scripts--> | ||
Latest revision as of 16:01, 22 August 2022
Description
STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
For details, please see the paper:
A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635 "STAR: ultrafast universal RNA-seq aligner"
Environment Modules
Run module spider star to find out what environment modules are available for this application.
System Variables
- HPC_STAR_DIR - installation directory
Additional Information
Make sure to set a directory for temporary files within your /blue working directory with the '--outTempDir argument to avoid job crashes and filling up diskless compute nodes. See Temporary Directories for more information.