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
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