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.

FILE FORMAT CHANGES

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• The status column in fpkm tracking files has been replaced by a per-condition quantification status column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