Question: mm9 gene names to mm10
0
gravatar for ravast
3.9 years ago by
ravast10
Netherlands
ravast10 wrote:

I have few gene name list (dont have genomic coordinates) which were aligned to mm9 reference genome.is there any way to convert these gene annotation to mm10 gene names. 

alignment genome • 2.1k views
ADD COMMENTlink modified 3.5 years ago by brianpenghe20 • written 3.9 years ago by ravast10
4
gravatar for karl.stamm
3.9 years ago by
karl.stamm3.5k
United States
karl.stamm3.5k wrote:

Gene names don't change between map revisions. Convert to a stable ID and continue ignoring coordinates. 

ADD COMMENTlink written 3.9 years ago by karl.stamm3.5k
3
gravatar for Ashutosh Pandey
3.9 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

Official gene symbols and gene ids remain the same between different assemblies for example, mm9 and mm10. There may be a few cases where a RIKEN clone may have been given a new name OR assigned to one of the already existing genes. Otherwise most of the gene names won't change between mm9 and mm10. 

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by Ashutosh Pandey11k
0
gravatar for brianpenghe
3.5 years ago by
brianpenghe20
United States
brianpenghe20 wrote:

You can get the mm9 coordinates of the genes,

then use this https://genome.ucsc.edu/cgi-bin/hgLiftOver

to convert the coordinates to mm10

and then get the annotations from there

ADD COMMENTlink written 3.5 years ago by brianpenghe20
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