galaxy with cuffdiff output
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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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:
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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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
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:
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===> 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
___________________________________________________________ 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:
-- 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:
participants (3)
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chenyao.bioinfor＠gmail.com -
Jennifer Jackson -
姚晨