Hello Sheena, If you concern with using the UCSC version of the database has to do with the chromosome naming and downstream Cufflinks analysis using Ensembl's reference GTF files, please see #5 on our FAQ, which demonstrates how to modify an Ensembl GTF file to be compatible with the UCSC chromosome naming (slight changes may be needed for each particular genome): http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq If there is another reason, please know that custom reference genomes (in fasta format) can be uploaded using FTP following this method: http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP Hopefully this helps, Best, Jen Galaxy team On 11/4/11 2:50 PM, Scroggins, Sheena wrote:

How do I upload the Zebrafish genome from Ensembl to my user history in Galaxy? I’m trying to map my RNA-Seq data using TopHat and need to map it to the Ensembl version of ZFv9, but Galaxy only has the UCSC version built in. The Ensembl version is slightly different. Thanks, Sheena

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