Difference between revisions of "Tophat"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m (Text replace - "{{#if: {{#var: mod}}|==Execution Environment and Modules== {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}" to "==Required Modules== modules documentation ===Serial=== *{{#var:app}}") |
|||
| (13 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:NGS]][[Category:Biology]][[Category:Sequencing]] |
| − | + | {|<!--Main settings - REQUIRED--> | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | {| | ||
| − | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|tophat}} | |{{#vardefine:app|tophat}} | ||
|{{#vardefine:url|http://tophat.cbcb.umd.edu/index.html}} | |{{#vardefine:url|http://tophat.cbcb.umd.edu/index.html}} | ||
| − | + | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | |
| − | |{{#vardefine: | ||
| − | |||
| − | |||
| − | |||
| − | |||
|{{#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--> | ||
| Line 38: | Line 23: | ||
<!--HPC pre-built Bowtie Indexes are located in ''/scratch/hpc/bio/bowtie''. They should be available for bowtie use automatically. If you have additional indexes that could be of use to UF Biological Community please contact us and we'll add them to the reference file space.--> | <!--HPC pre-built Bowtie Indexes are located in ''/scratch/hpc/bio/bowtie''. They should be available for bowtie use automatically. If you have additional indexes that could be of use to UF Biological Community please contact us and we'll add them to the reference file space.--> | ||
| − | + | <!--Modules--> | |
| − | + | ==Environment Modules== | |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | + | ==System Variables== | |
| − | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | |
| − | <!-- --> | ||
| − | == | ||
| − | |||
| − | == | ||
| − | *{{#var:app}} | ||
* HPC_TOPHAT_BIN - executable directory | * HPC_TOPHAT_BIN - executable directory | ||
* HPC_TOPHAT_DOC - documents directory | * HPC_TOPHAT_DOC - documents directory | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
| − | + | '''Note:''' If your data is compressed your job script should add another ppn to accommodate the external gzip process tophat will run. To be safe, add another ppn in any case. | |
| + | |}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
Latest revision as of 16:39, 22 August 2022
Description
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
Tophat is a part of the Tuxedo suite.
Environment Modules
Run module spider tophat to find out what environment modules are available for this application.
System Variables
- HPC_TOPHAT_DIR - installation directory
- HPC_TOPHAT_BIN - executable directory
- HPC_TOPHAT_DOC - documents directory
How To Run
Note: If your data is compressed your job script should add another ppn to accommodate the external gzip process tophat will run. To be safe, add another ppn in any case.