Difference between revisions of "STAR"

From UFRC
Jump to navigation Jump to search
 
(5 intermediate revisions by 2 users not shown)
Line 1: Line 1:
[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
+
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|star}}
 
|{{#vardefine:app|star}}
Line 5: Line 5:
 
<!--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-->
Line 24: Line 24:
 
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"
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
+
==Environment Modules==
===Serial===
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
Line 44: Line 34:
 
<!--Run-->
 
<!--Run-->
 
{{#if: {{#var: exe}}|==Additional Information==
 
{{#if: {{#var: exe}}|==Additional Information==
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+
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 website  

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.