Reference annotation GTF options for UCSC's mouse builds mm9, mm10

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Hello @Gaia_Gentile

Gencode annotation for the mouse builds mm9 and mm10 are available from the Gencode website.

Instructions for how to load and prepare that annotation for use with tools is covered in this prior Q&A. It is about a specific tool and the human genome, but the same advice applies:

You may also find this FAQ helpful:

I also added a few tags to your post that will lead to more related topics. Or, review the results of this search:

If that doesn’t answer you question, please explain more about the steps you have done so far (tools), and which data is involved (reference genome, reference annotation). If you are following a tutorial, include a link to that too please.

Thanks!