[BioMart Users] General query-Seems some of data come with wrong notations.

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[BioMart Users] General query-Seems some of data come with wrong notations.

Park, Hyun Jung
Dear BioMart team, 

I am trying to download miRNA of mm9 under Ensemble view. 
But when I download known (in terms of "Gene status") miRNAs (in terms of "Gene Biotype") for NCBIM37, 
some of them exceeds the range of mm9 chromosome. 

For example, it has the following line: 
Mir429 ENSMUSG00000065427 4 156053905 156053987 -1 E2 1 miRNA KNOWN. 
However, chr4 of mm9 ends earlier than that, going only up to 155630120.
Did you mean to say it is GRCm38, not NCBIM37?

HJ.



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[BioMart Users] Fwd: General query-Seems some of data come with wrong notations.

Park, Hyun Jung
<base href="x-msg://16/">If it's the case, then can you please let me know where I can download those for NCBIM37 (mm9)?

Thanks,
HJ.

Begin forwarded message:

From: "Park, Hyun Jung" <[hidden email]>
Date: March 21, 2013 2:56:57 PM CDT
Subject: General query-Seems some of data come with wrong notations.

Dear BioMart team, 

I am trying to download miRNA of mm9 under Ensemble view. 
But when I download known (in terms of "Gene status") miRNAs (in terms of "Gene Biotype") for NCBIM37, 
some of them exceeds the range of mm9 chromosome. 

For example, it has the following line: 
Mir429 ENSMUSG00000065427 4 156053905 156053987 -1 E2 1 miRNA KNOWN. 
However, chr4 of mm9 ends earlier than that, going only up to 155630120.
Did you mean to say it is GRCm38, not NCBIM37?

HJ.





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Re: [BioMart Users] Fwd: General query-Seems some of data come with wrong notations.

Rhoda Kinsella
Hi Hyun Jung
We released mouse GRCm38 in Ensembl release 68. In order to get the release 67 mouse NCBIm37m you will need to use our archive Ensembl BioMart database. Here is the link:


I hope that helps,
Kind regards
Rhoda


On 21 Mar 2013, at 19:57, "Park, Hyun Jung" <[hidden email]> wrote:

<base href="x-msg://16/">
If it's the case, then can you please let me know where I can download those for NCBIM37 (mm9)?

Thanks,
HJ.

Begin forwarded message:

From: "Park, Hyun Jung" <[hidden email]>
Date: March 21, 2013 2:56:57 PM CDT
Subject: General query-Seems some of data come with wrong notations.

Dear BioMart team, 

I am trying to download miRNA of mm9 under Ensemble view. 
But when I download known (in terms of "Gene status") miRNAs (in terms of "Gene Biotype") for NCBIM37, 
some of them exceeds the range of mm9 chromosome. 

For example, it has the following line: 
Mir429 ENSMUSG00000065427 4 156053905 156053987 -1 E2 1 miRNA KNOWN. 
However, chr4 of mm9 ends earlier than that, going only up to 155630120.
Did you mean to say it is GRCm38, not NCBIM37?

HJ.




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Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton,
Cambridge,
CB10 1SD




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