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Hi Jen,

I use tophat to align the RNA-seq data, then use cufflink ,cuffcompare
 and cuffdiff with a reference GTF fileto find differential expressed 
non-coding RNA.
But I don't know what is non-coding RNA track in the output file such as 
transcript.diff.
Are these "blank box" in the gene column denotes non-coding RNA?

Thank you
Chen Yao  


At 2011-08-26 01:29:24,"Jennifer Jackson" <j...@bx.psu.edu> wrote:
> ===> Please use "Reply All" when responding to this email! <===
>
> >   ===>  Please use "Reply All" when responding to this email!<===
>
>Hello,
>
>Without seeing your work history, it is difficult to know exactly which 
>steps/options are being used with the RNA-seq tools. However, I can let 
>you know that a reference GTF file can contain any transcript annotation 
>data that you want to use, including a non-coding RNA track.
>
>Some RNA-seq help
>http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
>http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq
>
>Hopefully this helps,
>
>Jen
>Galaxy team
>
>
>
>On 8/25/11 1:37 AM, 姚晨 wrote:
>>   ===>  Please use "Reply All" when responding to this email!<===
>>
>>
>>
>>
>> Dear all,
>>
>> I use cuffdiff in galaxy net version. The output are isoform.diff ,
>> gene.diff ...etc, but I want to find the differential expressed
>> non-coding RNAs. How can I get these information?
>>
>> Thank you
>>
>> Chen Yao
>>
>>
>>
>>
>> ___________________________________________________________
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>-- 
>Jennifer Jackson
>http://usegalaxy.org
>http://galaxyproject.org/Support
>___________________________________________________________
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___________________________________________________________
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