the refrence GTF file from Ensembl should have chr in the colum specifying 
Chrromosome number.
 
Vasu

--- On Thu, 3/31/11, Paul Korir <polaris...@gmail.com> wrote:


From: Paul Korir <polaris...@gmail.com>
Subject: Re: [galaxy-user] cufflinks FPKM
To: "lishiyong" <lishiy...@genomics.org.cn>
Cc: "galaxy-user" <galaxy-user@lists.bx.psu.edu>
Date: Thursday, March 31, 2011, 8:39 AM


Hi Li,

I think the solution lies in changing the chromosome names in the GTF file 
(refGene_hg18.gtf) from a number e.g. '1' to 'chr1'.

Paul


2011/3/31 lishiyong <lishiy...@genomics.org.cn>



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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www.paulkorir.com

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