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" <jen@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, Ò¦³¿ 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
>>
>>
>>
>>
>> ___________________________________________________________
>> 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/
>
>--
>Jennifer Jackson
>http://usegalaxy.org
>http://galaxyproject.org/Support
>___________________________________________________________
>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/