Hello, The workflow is available at this location: http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq5 The workflow specifically modifies Ensembl chromosome labels in a GTF file to be UCSC chromosome labels by adding a "chr" to the names ("1" -> "chr1"). This type of change is necessary when using any Ensembl data and the reference genome in Galaxy was sourced from UCSC (true for mm9, and most native Galaxy vertebrate genomes). The workflow will most likely work without any issues, but a double check of the result chromosome names would be recommended, as not all GTF files are created to the same specification. If needed, you should be able to modify the workflow (once imported into your account) to account for any additional changes needed. Best wishes for your project, Jen Galaxy team On 10/12/11 7:26 AM, shamsher jagat wrote:

I have read in the mailing list that you have a workflow which can modify the human GTF file so that it will be compatible with Top Hat. Will it also work with Ensembl mm9 GTF or there is a different work flow. Thanks

___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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

-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support