Question: Where can I download the NCBI reference genome for mouse GRCm38
1
gravatar for lojomorris
4.3 years ago by
lojomorris0
Germany
lojomorris0 wrote:

Hi,

I was wondering which NCBI reference genome assembly to use for mouse GRCm38, if I don't want to use the UCSC mm10. I thought the FTP-site of the Sanger mouse genomes project might be a good place to check: ftp://ftp-mouse.sanger.ac.uk/ref/ Does anyone know what the 68 refers to in the file name - GRCm38_68.fa? Many thanks, Lorna


 

assembly genome • 9.8k views
ADD COMMENTlink modified 4.3 years ago by Evgeniia Golovina990 • written 4.3 years ago by lojomorris0
1

68 is the Ensembl release that that was copied from.

ADD REPLYlink written 4.3 years ago by Devon Ryan92k
2
gravatar for Evgeniia Golovina
4.3 years ago by
New Zealand
Evgeniia Golovina990 wrote:

This is one, but from ensembl --> ftp://ftp.ensembl.org/pub/release-68/fasta/mus_musculus/dna/. Inappropriate?

This Ensembl version (release 68) corresponds to GRCm38 (mm10) (How To Display Old Assemblies Of The Mouse Genome In The Ensembl Genome Browser)

Some sorces to download mm10 genome version:
http://hgdownload-test.cse.ucsc.edu/goldenPath/mm10/bigZips/

http://www.ncbi.nlm.nih.gov/genome/52

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Evgeniia Golovina990

Thanks Evgeniia and Devon. I think ftp://ftp-mouse.sanger.ac.uk/ref/ is the same as ftp://ftp.ensembl.org/pub/release-68/fasta/mus_musculus/dna/ but it seems good practice to go to ensembl/UCSC/NCBI to download it.

ADD REPLYlink written 4.3 years ago by lojomorris0
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