Difference between revisions of "Cufflinks"
Jump to navigation
Jump to search
| (3 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]] |
{|<!--Main settings - REQUIRED--> | {|<!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|cufflinks}} | |{{#vardefine:app|cufflinks}} | ||
| Line 21: | Line 21: | ||
Cufflinks is a part of the [[Tuxedo]] suite. | Cufflinks is a part of the [[Tuxedo]] suite. | ||
<!--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_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
* HPC_CUFFLINKS_BIN - executable directory | * HPC_CUFFLINKS_BIN - executable directory | ||
* HPC_CUFFLINKS_DOC - readme directory | * HPC_CUFFLINKS_DOC - readme directory | ||
| Line 46: | Line 44: | ||
WRITE CITATION HERE | WRITE CITATION HERE | ||
|}} | |}} | ||
| − | |||
| − | |||
Latest revision as of 14:17, 15 August 2022
Description
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.
Cufflinks is a part of the Tuxedo suite.
Environment Modules
Run module spider cufflinks to find out what environment modules are available for this application.
System Variables
- HPC_CUFFLINKS_DIR - installation directory
- HPC_CUFFLINKS_BIN - executable directory
- HPC_CUFFLINKS_DOC - readme directory