Difference between revisions of "Tophat"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
|||
| (3 intermediate revisions by the same user 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}} | ||
| Line 24: | Line 24: | ||
<!--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--> | <!--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_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| Line 49: | Line 47: | ||
WRITE CITATION HERE | WRITE CITATION HERE | ||
|}} | |}} | ||
| − | |||
| − | |||
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.