Question: Mm9 Vs Mm10, Which One Is Better For Mouse Reference
2
gravatar for Tonyzeng
6.0 years ago by
Tonyzeng300
Tonyzeng300 wrote:

My question is that I read most of the mouse sequence paper, there is no one use mm10 as reference for alignment, and seems like mm10 has fewer annotation compared with mm9, is that true? Has anyone use mm10 for alignment and get a good result?

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ADD COMMENTlink modified 6.0 years ago by Ido Tamir5.0k • written 6.0 years ago by Tonyzeng300
6
gravatar for Ido Tamir
6.0 years ago by
Ido Tamir5.0k
Austria
Ido Tamir5.0k wrote:

Thats becaue most people have started accumulating data, insight etc... with mm9 and are reluctant to map, annotate etc.. everything again. Then there is the data produced by other you would like to compare with, e.g. ENCODE and thats also on mm9.

What are the differences, what do you gain? http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/data/ no tables here in markdown?

mm9: Total Bases in Assembly 2,745,142,291 Total Non-N Bases in Assembly 2,648,522,751

mm10: Total Bases in Assembly 2,798,785,524 Total Non-N Bases in Assembly 2,719,482,043

so 70million more bases in assembly, that 1/2 a chromosome. There are much less unplaced scaffold, for most chromosomes they think they are completeley assembled. Then there is the PAR region for X and Y chromosomes.

Then there is the annotation. Ensembl and I think UCSC (? maybe yes) does not backport their new annotation, so this is something you loose - novel miRNAs, lincRNAs etc...

ADD COMMENTlink written 6.0 years ago by Ido Tamir5.0k
1

mm10 annotation will catch up eventually. There was a similar issue with the human genome; hg19 used to be much less complete compared with hg18 but now most people have moved to hg19. It's just a function of when you start work compared with time since last release in the build cycle.

ADD REPLYlink written 6.0 years ago by Neilfws48k

+1 Really nice answer.

ADD REPLYlink written 6.0 years ago by PoGibas4.8k
1
gravatar for Ashutosh Pandey
6.0 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

mm10 is better for alignment based (more reads are mapped) on personal experience. Also, it has been a while since mm10 is out so its the right time to make the transition. All the gene models including UCSC, RefSeq and Ensembl are available for mm10. And for other annotations you can always liftOver mm9 to mm10.

ADD COMMENTlink written 6.0 years ago by Ashutosh Pandey11k

Also, mm9 has lot of nucleotide base errors that have been corrected in mm10.

ADD REPLYlink written 6.0 years ago by Ashutosh Pandey11k
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