Question: Where can I download mouse genemodels files to use in ChIP-seq analysis
0
gravatar for fhassanz
4.7 years ago by
fhassanz20
fhassanz20 wrote:

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,

chip-seq gene models mm9 • 1.1k views
ADD COMMENTlink modified 4.7 years ago by Sinji3.0k • written 4.7 years ago by fhassanz20
0
gravatar for Sinji
4.7 years ago by
Sinji3.0k
UT Southwestern Medical Center
Sinji3.0k wrote:

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.

ADD COMMENTlink written 4.7 years ago by Sinji3.0k

Thank you very much Sinji!

ADD REPLYlink written 4.7 years ago by fhassanz20
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