Cufflinks 1.1.0 released

This is a fix release to address several issues reported by our users:

  • Cuffdiff now includes a more sophisticated check for sufficient sequencing depth prior to testing for differences, which substantially improves the accuracy of differential expression analysis in loci with low to medium depth.
  • A bug in the calculation of the parameters for the beta negative binomial distribution used during variance estimation has been fixed.
  • Some users have reported that Cufflinks or Cuffdiff crashes due to running out of memory when processing highly expressed loci. Both programs now have a maximum number of fragments that can fall within a locus. If a locus has more than this maximum, it is skipped. The threshold is configurable via the –max-bundle-frags option.
  • Gffread now keeps the longest CDS when collapsing transcripts.


  • By popular request, 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  • The status column in fpkm tracking files has been replaced by a per-condition quantification status column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.