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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