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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




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