Hi lishiyong,

Most likely your refGene_hg18.gtf file is not sorted correctly.  You have to 
sort by chr and then by start coordinate.

From: lishiyong [lishiy...@genomics.org.cn]
Sent: Thursday, March 31, 2011 3:39 AM
To: galaxy-user
Subject: [galaxy-user] cufflinks FPKM


       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 - 
(3) cufflinks -G refGene_hg18.gtf test.bam.bam

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