I have read in the mailing list that you have a workflow which can
the human GTF file so that it will be compatible with Top Hat. Will it
work with Ensembl mm9 GTF or there is a different work flow.
The workflow is available at this location:
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
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,