Cufflinks
Overview
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.
Version 2.2.1 and 2.1.1 binaries are available on the iCSF.
Restrictions on use
All users may access and use Cufflinks. The software is open source. Users should consult the Boost Software License 1.0 for further information.
Set up procedure
To access the software load one of the following modulefiles for the version you require:
module load apps/binapps/cufflinks/2.2.1 module load apps/binapps/cufflinks/2.1.1
Running the application
It may be necessary to use other applications in conjunction with Cufflinks.
Panagiotis Papastamoulis, from FLS has very kindly provided some documentaion illustrating how to use Cufflinks on the CSF, (note CSF, not iCSF) in conjunction with other tools and including example jobscripts. On the iCSF you don’t need to use jobscripts – you can simply run the commands specified in the jobscripts directly on the iCSF node you have been logged in to.
Troubleshooting
You may see the following error when using cufflinks, but it is nothing to worry about and the software will still run.
cufflinks: /lib64/libz.so.1: no version information available (required by cufflinks)
Further info
- The Cufflinks website has a manual, FAQ and index and annotations downloads.
- Related applications available on the iCSF: