danrer7 vs zv9 assembly

[Santanu Banerjee]

Dear UCSC genome browser staff,

I recently aligned zebrafish RNA seq data to danrer7 from UCSC. I saw there are  14417 genes in danrer7. However when I aligned the same data onto zv9 (from ensemble) I found over 35,513 genes.

I am very new to this analysis and kind of puzzled by this as I thought zv9 and danrer7 are same versions of zfish genome. Is the difference I see due to different gene/mRNA annotation files where zv9 has more annotated genes or the DNA sequence information is different between danrer7 and zv9.

Many thanks for your help!

Santanu

--

[Cath Tyner]

​Hello Santanu,

Thank you for submitting your question regarding alignment differences among danRer7/zv9 assemblies. 

Can you reply to this list and let me know which gene set you are aligning, and describe your alignment method?

​

I

​can confirm that the UCSC 

danRer7

​assembly

 is indeed equivalent to

​:

​

Jul. 2010 zebrafish (Danio rerio) Zv9 assembly (GCA_000002035.2):
http://www.ncbi.nlm.nih.gov/assembly/238918/

​Please

 verify that

​you

 are using the

​ensembl ​

assembly which corresponds to GenBank Assembly ID GCA_000002035.2:
http://mar2015.archive.ensembl.org/index.html
http://mar2015.archive.ensembl.org/Danio_rerio/Info/Index

​A​

s noted on http://mar2015.archive.ensembl.org/Danio_rerio/Info/Annotation
"Zv9 (GCA_000002035.2) is the ninth integrated assembly of the zebrafish genome. This assembly is used by UCSC to create their danRer7 database."

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

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 genome...@soe.ucsc.edu 

or search the Mirror Archives​

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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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