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

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

--
Paul Korir
www.paulkorir.com

-----Inline Attachment Follows-----

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/