Difference between revisions of "Applications/Cufflinks"
From HPC
m |
m |
||
| Line 33: | Line 33: | ||
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
| − | [username@login01 ~]$ module | + | [username@login01 ~]$ module add cufflinks/2.2.1 |
</pre> | </pre> | ||
Revision as of 13:26, 7 June 2018
Application Details
- Description: The Cufflinks suite of tools can be used to perform a number of different types of analyses for RNA-Seq experiments. The Cufflinks suite includes a number of different programs that work together to perform these analyses.
- Version: 2.2.1
- Modules: cufflinks/2.2.1
- Licence: Open source (Github)
Usage Examples
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.
It provides the following tools:
- cuffcompare
- cuffdiff
- cufflinks
- cuffmerge
- cuffnorm
- cuffquant
- gffread
- gtf_to_sam
With linkages to the following modules too:
[username@login01 ~]$ module add cufflinks/2.2.1
Further Information
|