Hi Jen,

Thanks for your reply! I know this workflow.  I am just wondering if there
is a tool in Galaxy to combine the reads that mapped to the same gene with
different positions before running cufflinks. 

Thanks again,

Yan


-----邮件原件-----
发件人: Jennifer Jackson [mailto:j...@bx.psu.edu] 
发送时间: Wednesday, August 15, 2012 11:01 AM
收件人: Yan He
抄送: galaxy-user@lists.bx.psu.edu
主题: Re: [galaxy-user] how to sort mapped data?

Hello Yan,

To sort a SAM file produced by Bowtie before using it with Cufflinks (a
requirement), please see this FAQ and workflow:

http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2

Best,

Jen
Galaxy team

On 8/14/12 7:33 PM, Yan He wrote:
> Hi everyone,
>
> I am working on RNA-seq data. First, I mapped the reads to the 
> reference transcriptome using bowtie. I found some different reads 
> mapped to the same gene with different positions. Before running 
> Cufflinks,  I would like to combine the reads  that mapped to the same 
> gene though with different positions. Is there a tool in Galaxy can
fulfill this purpose?
> Any suggestion would be much appreciated. Thanks!
>
> Yan
>
>
>
> ___________________________________________________________
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--
Jennifer Jackson
http://galaxyproject.org


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