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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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