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Question: Galaxy With Cuffdiff Output
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gravatar for 姚晨
7.3 years ago by
姚晨 • 10
姚晨 • 10 wrote:
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
galaxy • 1.4k views
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modified 7.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.3 years ago by 姚晨 • 10
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gravatar for Jennifer Hillman Jackson
7.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD COMMENT • link written 7.3 years ago by Jennifer Hillman Jackson ♦ 25k
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
ADD REPLY • link written 7.3 years ago by yao chen • 50
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