Question: Difference between genome subreleases?
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gravatar for Nathaniel
3.6 years ago by
Nathaniel70
Denmark
Nathaniel70 wrote:

Each major genome version has several subreleases, which you can see here: http://www.ensembl.org/info/website/archives/assembly.html. For instance, the mouse has the following for the mm10 genome: GRCm38.p4 GRCm38.p3 GRCm38.p2 GRCm38.p1

My problem: I have a some data which is annotated with the Ensemble version 84, which was done on GRCm38.p4. Now I need to extract the sequences for each gene, and I am using the following R package, which was generated in 2011, with the first subrelease of the genome (GRCm38.p1 I guess): http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Mmusculus.UCSC.mm10.html

Can I simply do that, or I need to extract the sequence specifically for GRCm38.p4?

So more precisely, my questions are: (Q) What is the difference between the genome subreleases? Can they be used interchangeably without major concerns? Do the genomic coordinates differ between subreleases?

assembly genome • 2.1k views
ADD COMMENTlink modified 3.6 years ago by genomax72k • written 3.6 years ago by Nathaniel70
0
gravatar for genomax
3.6 years ago by
genomax72k
United States
genomax72k wrote:

See the definition of "patches" on GRC help page.

Patches are accessioned scaffold sequences that represent assembly updates. They add information to the assembly without disrupting the chromosome coordinates.

ADD COMMENTlink written 3.6 years ago by genomax72k

Great, thanks for the reply!

ADD REPLYlink written 3.6 years ago by Nathaniel70
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