Where can I download mouse genemodels files to use in ChIP-seq analysis

Question

[fhassanz]

I want to intersect my ChIP-seq data (peaks) to mouse Genemodels (a
 collection
 of
 introns
 and
 exons
 and
 their
 locations
 in
 the
 genomic
 sequence). I used mm9 data in the alignment step. I would appreciate if you can tell me where I can download the genemodel file that I can use in my analysis.

Thanks,

Answer 1

[Sinji]

Head over to the UCSC Table Browser.

1. Change 'genome' to Mouse.
2. Change 'assembly' to July 2007 (NCBI37/mm9)
3. Change 'track' to RefSeq Genes
4. Change 'output format' to GTF - gene transfer format
5. Type a name for your file in 'output file'.
6. Click on 'get output'.

You can then use awk or grep to obtain a list of introns / exons or regions you are interested in.

[fhassanz]

Thank you very much Sinji!