Hello Susan The tool is using the identifier in the "gene_id" attribute from the reference annotation GTF to name the output. This link at the tool manual can help: http://cufflinks.cbcb.umd.edu/howitworks.html#hdif The iGenomes dataset may be what you are looking for. "Shared Data -> Data Libraries -> iGenomes" has the mm9 gene.gtf file loaded already. Other genomes will be added near term. Example of mm9 iGenomes GTF (note that gene_id is the gene symbol): chr1 unknown exon 3204563 3207049 . - . gene_id "Xkr4"; transcript_id "NM_001011874"; gene_name "Xkr4"; p_id "P2739"; tss_id "TSS1881"; For now, you can download and open the archive yourself (locally), then load just the genes.gtf file to Galaxy, if your genome is in the list. http://cufflinks.cbcb.umd.edu/igenomes.html Best, Jen Galaxy team On 8/17/12 6:42 AM, suzan katie wrote:

Hello,

I am new to using Galaxy tools. I am running paired end RNA-Seq data on Galaxy and I want to differential gene expression between control and treated samples

I was fine until running TopHat output, I am having problems with cufflinks and cuffdiff output.

I ran the cufflinks and cuffdiff twice, once with reference annotation and once without reference annotation (Imported form UCSC). Output with reference annotation produced output with gene ids naming usc## Output without reference annotation produced output with gene ids naming CUFF1.###

Can anyone suggest how to get gene names instead of just numbers?

Thanks

suz

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