Can you tell me which version of Tophat and Cufflinks is being used and whether the Tophat you have uses a GFF or GTF file to help it find splices (this is an option I believe)?
Best Wishes, David
__________________________________ Dr David A. Matthews
Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K.
Tel. +44 117 3312058