This release addresses several bugs, most of which were introduced as part of the 2.0.0 release:
- Some users were experiencing a problem with the Linux pre-compiled binary packages where Cuffdiff was reporting many genes and transcripts as having expression levels of zero or “nan” or “inf”. This was determined to be caused by a recent change in the binary packaging process we use to distribute pre-compiled binaries.
- Multi-read correction in Cuffdiff 2.0 was not always being applied when the user specified -u/–multi-read-correct.
- Some rarely encountered GTF parsing issues have been corrected.
- Effective length correction can be disabled in Cufflinks and Cuffdiff with the new –no-effective-length-correction option.