Cufflinks Files

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 outputs several files:

  • transcripts.gtf - can be viewed in IGV 2.0
  • transcripts.expr - support for this file is in progress
  • genes.expr - can be viewed in IGV 2.0