I am having trouble running cufflinks with an annotation file on the public 
Galaxy.  The assembled transcripts gtf file has all the FPKM at 0 although the 
gene expression and transcript expression tab files have values for FPKM.

I have seen the SEQanswers threads about the compatibility of tophat bam files 
relative to chromosomes labeled as 1,2,3… versus Chr1, Chr2, Chr3…   I am using 
the iGenomes bovine UMD3.1 genome and annotation file (chromosomes are  1,2,3) 
from the history.  I altered the gtf file to Chr1, Chr2, Chr3… but it did not 

Another potential discrepency/conflict is that the genome and gtf file have the 
bosTau6 database attribute from when I uploaded them. However I am running them 
from the history (bosTau6 is not an option for tophat).  I do not seem to be 
able to remove the attribute.

Am I missing something else?

Here is the command line
Info: cufflinks v1.0.3
cufflinks -q --no-update-check -I 50000 -F 0.050000 -j 0.050000 -p 8 -G 
/galaxy/main_database/files/003/142/dataset_3142240.dat -N -b ref.fa

Here is the details page
Tool: Cufflinks
Name: Cufflinks on data 69, data 4, and data 5: assembled transcripts
Created: Nov 09, 2011
Filesize: 44.6 Mb
Dbkey: bosTau6
Format: gtf
Tool Version:
Input Parameter  Value
SAM or BAM file of aligned RNA-Seq reads  4: Tophat for Illumina on data 4 and 
data 69: accepted_hits
Max Intron Length  50000
Min Isoform Fraction  0.05
Pre MRNA Fraction  0.05
Perform quartile normalization  Yes
Conditional (reference_annotation)  1
Reference Annotation  5: iGen_UMD3_1_genes.gtf
Conditional (bias_correction)  0
Conditional (seq_source)  1
Using reference file  69: UMD31_iGen_1-29X.fa
Conditional (singlePaired)  0


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