Cufflinks¶
Description¶
Cufflinks is a part of the "Tuxedo" suite of programs. 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. FILE FORMAT CHANGES: * Fold changes are now reported log2, rather than natural log. * The status column in fpkm tracking files has been replaced by a per-condition quantification status column. * The header size limit in Cufflinks' BAM parser used to have a 4 megabyte limit. This has been removed to allow Cufflinks to be used on assemblies with many contigs.
Environment Modules¶
Run module spider cufflinks to find out what environment modules are available for this application.
Environment Variables¶
- HPC_CUFFLINKS_DIR - installation directory
- HPC_CUFFLINKS_BIN - executable directory
- HPC_CUFFLINKS_DOC - documents directory
Categories¶
biology, ngs, sequencing