Question: Where can I get the mouse mm9 gene annotation file?
0
gravatar for Avro
5.4 years ago by
Avro140
Canada
Avro140 wrote:

Hi everyone,

I know that it sounds trivial, but I have been looking around (e.g. UCSC) for the mouse mm9 gene annotation file, and I can't get a clear fie with gene ID and genomic locations. I keep getting raw sequence files, alignment files,...

For example, with the Broad's IGV, you can put a gene name for mm9, and you the exact gene location. Hence, does anyone know how to get such file (e.g. from the Broad)? Or do I have to somehow build it myself?

Thank you.

 

 

 

 

annotation mm9 • 11k views
ADD COMMENTlink modified 5.4 years ago by balaji40 • written 5.4 years ago by Avro140
2
gravatar for Istvan Albert
5.4 years ago by
Istvan Albert ♦♦ 82k
University Park, USA
Istvan Albert ♦♦ 82k wrote:

There are various resources, for example see this post Download gene names and annotations *.gff

Also look for similar posts in the right sidebar

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by Istvan Albert ♦♦ 82k
2
gravatar for balaji
5.4 years ago by
balaji40
Estonia
balaji40 wrote:

From biomart you can download all annotations for mm9 or other builds or versions. Here is the link for from where you can download for all genes or for your genes of interests have a look at filters for your genes.

http://may2012.archive.ensembl.org/biomart/martview/

ADD COMMENTlink written 5.4 years ago by balaji40

Thank you! I appreciate your time! 

ADD REPLYlink written 5.4 years ago by Avro140
1
gravatar for Ming Tang
5.4 years ago by
Ming Tang2.5k
Houston/MD Anderson Cancer Center
Ming Tang2.5k wrote:

you can get the gff file here http://www.gencodegenes.org/

or here ftp://ftp.ensembl.org/pub/

 

ADD COMMENTlink written 5.4 years ago by Ming Tang2.5k
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