Difference between revisions of "Cufflinks"
Moskalenko (talk | contribs) (Created page with "__NOTOC__ __NOEDITSECTION__ Category:SoftwareCategory:Bioinformatics <!-- ######## Template Configuration ######## --> <!--Edit definitions of the variables used in temp...") |
Moskalenko (talk | contribs) |
||
| Line 33: | Line 33: | ||
{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | ||
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 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. | ||
<!--Location--> | <!--Location--> | ||
{{App_Location|app={{#var:app}}|{{#var:ver}}}} | {{App_Location|app={{#var:app}}|{{#var:ver}}}} | ||
Revision as of 20:43, 15 November 2011
Description
{{{name}}} website
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. Template:App Location
Available Versions
- 1.0.3
- 1.1.0 - Default - (Beware the file format change)
Running the application using modules
To use cufflinks with the environment modules system at HPC the following commands are available:
Get module information for cufflinks:
$module spider cufflinks
Load the default application module:
$module load cufflinks
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_CUFFLINKS_DIR - directory where cufflinks is located.
- HPC_CUFFLINKS_BIN - executable directory
- HPC_CUFFLINKS_DOC - readme directory