Difference between revisions of "FragGeneScan"
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|{{#vardefine:app|fraggenescan}} | |{{#vardefine:app|fraggenescan}} | ||
|{{#vardefine:url|http://omics.informatics.indiana.edu/FragGeneScan/}} | |{{#vardefine:url|http://omics.informatics.indiana.edu/FragGeneScan/}} | ||
| − | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | + | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> |
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | ||
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===Serial=== | ===Serial=== | ||
*{{#var:app}} | *{{#var:app}} | ||
| + | ==System Variables== | ||
| + | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
* HPC_FRAGGENESCAN_BIN - executable directory. | * HPC_FRAGGENESCAN_BIN - executable directory. | ||
| + | <!--Additional--> | ||
| + | {{#if: {{#var: exe}}|==Additional Information== | ||
Two convenience scripts are provided within the FragGeneScan distribution - run_FragGeneScan.pl and post_process.pl - in addition to the main FragGeneScan binary. | Two convenience scripts are provided within the FragGeneScan distribution - run_FragGeneScan.pl and post_process.pl - in addition to the main FragGeneScan binary. | ||
Read the [http://omics.informatics.indiana.edu/FragGeneScan/README usage documentation] for details on how to run the program. | Read the [http://omics.informatics.indiana.edu/FragGeneScan/README usage documentation] for details on how to run the program. | ||
| + | }} | ||
{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
Mina Rho, Haixu Tang, and Yuzhen Ye. FragGeneScan: Predicting Genes in Short and Error-prone Reads. Nucl. Acids Res., 2010 doi: [http://nar.oxfordjournals.org/content/early/2010/08/29/nar.gkq747.abstract 10.1093/nar/gkq747] | Mina Rho, Haixu Tang, and Yuzhen Ye. FragGeneScan: Predicting Genes in Short and Error-prone Reads. Nucl. Acids Res., 2010 doi: [http://nar.oxfordjournals.org/content/early/2010/08/29/nar.gkq747.abstract 10.1093/nar/gkq747] | ||
|}} | |}} | ||
Revision as of 18:25, 10 August 2012
Description
FragGeneScan is an application for finding (fragmented) genes in short reads.
Required Modules
Serial
- fraggenescan
System Variables
- HPC_{{#uppercase:fraggenescan}}_DIR - installation directory
- HPC_FRAGGENESCAN_BIN - executable directory.
Additional Information
Two convenience scripts are provided within the FragGeneScan distribution - run_FragGeneScan.pl and post_process.pl - in addition to the main FragGeneScan binary.
Read the usage documentation for details on how to run the program.
Citation
Mina Rho, Haixu Tang, and Yuzhen Ye. FragGeneScan: Predicting Genes in Short and Error-prone Reads. Nucl. Acids Res., 2010 doi: 10.1093/nar/gkq747