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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