If Cufflinks works without a reference GTF, then the problem is the mismatch 
b/t your GTF and your bam file. A couple things to check:

(1) that your genome chrom names in F3.csfata match those in your GTF; if not, 
you'll need to modify your GTF to match the names in your fasta.
(2) that your GTF is sorted as your BAM is sorted.

If these issues don't solve your problem, it's best to use the Cufflinks help 
email that I noted in my previous email.

Good luck,
J.
        
On Mar 31, 2011, at 10:32 AM, lishiyong wrote:

>  
> Hello,I don't use Galaxy.But I have uploaded the file(sorted file  
> 20:test_44.bam  refgene.gtf : ) It's works OK without the reference GTF file 
> ,while with reference, I can't gain the right results, I do these in my 
> computer.
> 2011-03-31
> lishiyong
> 发件人: Jeremy Goecks
> 发送时间: 2011-03-31  21:36:52
> 收件人: lishiyong
> 抄送: galaxy-user
> 主题: Re: [galaxy-user] cufflinks FPKM
> Hello,
> 
> It's not clear whether you're using Galaxy. If you're using Galaxy, please 
> share you history with me (History Options --> Share/Publish --> Share with 
> User --> my email) and I'll take a look; otherwise, Cufflinks has an email 
> list for questions: tophat.cuffli...@gmail.com
> 
> Best,
> J.
> 
> On Mar 31, 2011, at 3:39 AM, lishiyong wrote:
> 
>> Hi:
>>  
>>  
>>        I gain the SOLiD sequencing data.I used bowtie to map human genome 
>> then I sort the sam file .I used cuffinks to calculate FPKM with the sam 
>> file ,human gtf file .it gives 0 FPKM values and this is for all genes 
>> .what's the reason?
>>  
>> (1) bowtie -C human_hg18_color -f F3.csfasta -Q F3_QV.qual -v 2 -k 100 -p 6 
>> --mapq  --sam test.sam
>> (2) samtools view -uS test.sam  2>/dev/null  | samtools sort -m 2000000000 - 
>> test.bam
>> (3) cufflinks -G refGene_hg18.gtf test.bam.bam
>> 2011-03-31
>> lishiyong
>> ___________________________________________________________
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> 
> 

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