the refgene.gtf have chr in the first colum. and I also sorted it.
2011-03-31

lishiyong

发件人: vasu punj
发送时间: 2011-03-31  22:26:36
收件人: lishiyong; Paul Korir
抄送: galaxy-user
主题: Re: [galaxy-user] cufflinks FPKM
the refrence GTF file from Ensembl should have chr in the colum specifying Chrromosome number.
 
Vasu

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

From: Paul Korir <polariseke@gmail.com>
Subject: Re: [galaxy-user] cufflinks FPKM
To: "lishiyong" <lishiyong@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 <lishiyong@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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