We are happy to announce a major update to Cufflinks that introduces some powerful new features and includes a number of performance improvement and bug fixes. Highlights include:
We hope you find the new functionality useful, and continue to report bugs and feature requests.
- Cufflinks now includes a new tool, "Cuffdiff", which performs testing for differential expression, splicing, promoter use, and coding sequence output on two or more RNA-Seq samples. See the greatly expanded manual for details.
- Cuffcompare now reports a file containing the "union" of all transfrags in the files you give it as input, greatly simplifying downstream validatation of novel transcripts.
- Cufflinks' assembler has been overhauled and optimized, resulting in a speedup of 4-5 times over version 0.7.0, and a greatly reduced memory footprint. Phasing of splicing events has also been improved.
- Many bugfixes, including for a number of bugs reported by users in these forums.
We hope you find the new functionality useful, and continue to report bugs and feature requests.
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