Cufflinks 0.8.2 released

Numerous bug fixes and significant performance improvements in Cufflinks and Cuffdiff. Note that some the formats of some files have changed. Other changes:

  • Expression values were not being reported for a small number of genes when using certain annotation files.
  • Fixed a divide-by-zero error in Cuffdiff
  • Various GTF parser fixes.
  • .expr files produced by Cufflinks now contain FPKM confidence interval columns
  • Isoform filtering was being innappropriately applied when working with annotation in Cufflinks (via –GTF)
  • The .tmap files reported by Cuffdiff contained zero in FPKM field.
  • New command line options –num-importance-samples and –max-mle-iterations allow advanced users to influence of the transcript abundance estimation.