Difference between revisions of "Tophat"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) |
Moskalenko (talk | contribs) |
||
| Line 33: | Line 33: | ||
* 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. | + | '''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== | ||
Revision as of 20:16, 16 May 2013
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.
Required Modules
Serial
- tophat
System Variables
- HPC_{{#uppercase: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.