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


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

   http://lists.bx.psu.edu/


--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/

Reply via email to