Hello Jiwen,

For Cufflinks to incorporate reference transcript and gene annotation (known gene names, as opposed to experimentally assigned labels), a correctly formatted reference GTF file will need to be used.


This tutorial shows how this type of information is incorporated using the Cufflinks tool form:
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise

And this FAQ can help with common troubleshooting:
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq

Where to obtain a reference annotation GTF file can vary depending on the genome you are working with. The tool authors are a good resource to ask about potential sources. Contact information is in the "Example" RNA-seq" section of this wiki:
http://wiki.g2.bx.psu.edu/Support#Unexpected_scientific_result

Best wishes for your project,

Jen
Galaxy team

On 1/31/12 8:57 AM, 杨继文 wrote:
Hi all,
I am learning how to use Galaxy to analyze my RNA-Seq data. After
running cuffdiff, one of the files I got is "transcript differential
expression testing <javascript:void(0);>". In this file, I can see "

gene_id" is something like "XLOC_000001". I am wondering how I can find the 
name of differentially expressed genes and transcripts.

Can anyone help me??????

Thanks in advance.

Jiwen









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