Cufflinks
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.
License
Boost Software License, Version 1.0
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of cufflinks and load default version of cufflinks as
module avail cufflinks/ # list available modules module load cufflinks # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail cufflinks
and choose explicit version you want to use.
Parallel runs
Cuffdiff is not parallellized very well and bias correction is very slow for long transcripts, we recommend two stage processing using separate single-processor jobs for each sample
cuffquant -o S1_q -b ALL.fa merged.gtf S1/accepted_hits.bam
and then final (single-processor as well)
cuffdiff -o exp -b ALL.fa -L Cond1,Cond2 -u merged.gtf S1_q/abundances.cxb S2_q/abundances.cxb,S3_q/abundances.cxb
Documentation
http://cufflinks.cbcb.umd.edu/