Difference between revisions of "Applications/Cufflinks"
From HPC
m (Pysdlb moved page Cufflinks to Applications/Cufflinks without leaving a redirect) |
m |
||
| Line 25: | Line 25: | ||
* Tophat | * Tophat | ||
| − | * Samtools | + | * [[applications/Samtools|Samtools]] |
| − | |||
<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;"> | ||
Revision as of 15:32, 5 April 2017
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:
- Tophat
- Samtools
[username@login01 ~]$ module load cufflinks/2.2.1
Further Information
|