#What is Cufflinks?

#How does Cufflinks assemble transcripts?

#How does Cufflinks calculate transcript abundances?

#How does Cufflinks estimate the fragment length distribution?

#How does Cufflinks identify and correct for sequence bias?

#How does Cufflinks handle multi-mapped reads?

#How does Reference Annotation Based Transcript (RABT) assembly work?

#What is Cuffdiff?

#How does Cuffdiff test for differentially expressed and regulated genes?

#What’s changed since the paper was published?