Reg genome mm9 and mm10

[kishore Reddy]

Dear team Genome Browser,

I am new to bio informatics and we are planning to align rnaseq data. Shall we go ahead with mm9 or mm10.
I didn't find much information or specifically the comparisons for both the genome assemblies.
Subsequently we are also going to generate human data so it's it hg19 or hg38.

Can you please help on this.

Best,
Reddy

[Cath Tyner]

Hello Reddy,

Thank you for your interest in using the UCSC Genome Browser and for submitting your question regarding general assembly information.

The best place to start learning more about assembly versions is the assembly description pages in the UCSC Genome Browser. For mouse, the most recent assembly version is mm10, and for human, the most recent version is hg38.

From the assembly gateway pages listed below, you can click the "GO" button to go to the browser for each assembly. There you will see many data tracks for each assembly. If you click on underlined name of each track, you will go to the track description page. For example, you can go to the mm10 gateway page, click "GO" to get to the browser, and then click on the track labeled, "UCSC Genes" to learn more.

Mouse assembly gateway pages for mm10 & mm9.

Human assembly gateway pages for hg38 & hg19.

While it is outside the scope of this mailing list to make recommendations regarding which assembly you should use, you might want to visit Bioinformatics forums, such as Biostars:

​Biostars ​

Question: Mm9 Vs Mm10, Which One Is Better For Mouse Reference

You can also search our public mailing list archives. For example, you could search "RNA-seq" and "mm9".

You can search our news page for keywords like "mm10" to see announcement details. For example:

28 May 2015 - New UCSC Genes Track Released for GRCm38/mm10
We're happy to announce the release of an updated UCSC Genes track for the GRCm38/mm10 mouse Genome Browser. The new release has 63,244 total transcripts, compared with 61,642 in the previous version. The total number of canonical genes has increased from 32,408 to 32,958. Comparing the new gene set with the previous version:
59,119 transcripts did not change between versions.
55 transcripts were not carried forward to the new version.
2,308 transcripts are "compatible" with those in the previous set, meaning that the two transcripts show consistent splicing. In most cases, the old and new transcripts differ in the lengths of their UTRs.
160 transcripts overlap with those in the previous set, but do not show consistent splicing (i.e., they contain overlapping introns with differing splice sites).

Finally,

​ i​

f you are new to the UCSC Genome Browser, you might also be interested in some introductory video tutorials about the browser available from our training page

​ and on Open Helix. 

Thank you again for your inquiry and for using the UCSC Genome Browser. 

​Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:

  * Post to the Public Help Forum: E

mail 

gen...@soe.ucsc.edu

​ or search the Public Archives

​  * Post to the Mirror Help Forum: Email

 genome...@soe.ucsc.edu 

or search the Mirror Archives​

​  * Confidential/private data help: Email

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​Enjoy,

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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