This release includes two bug fixes and some enhancements for strand-specific RNA-Seq libraries:
- SAM files without headers, such as those produced by TopHat 1.0.14 and earlier, were being erroneously reported as unsorted during GTF-based quantification, causing Cufflinks and Cuffdiff to exit. This has been fixed, so that SAM files are now correctly handled, restoring compatibility with output from TopHat 1.0.14 and earlier.
- Cufflinks and Cuffdiff were sometimes producing different FPKM values for minor isoforms when run on the same sample. They are now consistent, and should agree on isoform abundance calls.
- Strand-specific, single end libraries are now supported. Some library type names have changed to reflect the expanded list of supported protocols.