Hi, Galaxy user. I ran into a problem when using Cuffdiff 1.2.1 in Galaxy local instance to check differential expressed genes in my samples. I have 3 normals and 6 cancers samples, I did the following: - After tophat for each samples, run cufflink with refseq annotation which has 25266 genes and 43091 transcripts - cuffmerge all cufflink outputs contains 58112 lines - run cuffdiff with 3 normals as triplicate and compare to each cancer sample. Suprisingly, I fould out that the tanscripts tracking file, gene tracking, CDS tracking only has 2000 genes and 4000 transcripts. So the cufflink only compare 2000 genes and 4000 transcripts between samples. The question I want to ask here is that *why are the rest of the genes and transcripts not being tested and included in the tracking files?* Do you know what cause this kind of problem? Thanks, Wei