[BioMart Users] Request

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[BioMart Users] Request

Juan Martinez

Dear Arek,

        First we would like to thank you for Biomart, is a fantastic tool for non-experts.
We have a huge dataset (Chipseq data) mapped on an older version of the zebrafish genome (zv8) and we would like to link it to some BIomart data, which works only with zv9. Currently Biomart can transform the GENOMIC POSITIONS  of genes annotated in zv8 to zv9, but NOT conversely.

        We would appreciate any suggestions to go around this problem without loosing too many data.

Thanks a lot in advance for your help,

Juan


Juan Ramón Martínez Morales
Centro Andaluz de Biología del Desarrollo (CABD)
(Andalusian Centre for Developmental Biology)
CSIC-Universidad Pablo de Olavide
Carretera de Utrera, Km1
41013 Sevilla, Spain
+34954977827
[hidden email]






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Re: [BioMart Users] Request

Arek Kasprzyk
Hi Juan,
could you elaborate more on BioMart 'translating genomic positions' of genes from zv8 to zv9?
I am unclear what you mean by that


cheers,
a



On Fri, Sep 16, 2011 at 6:53 AM, Juan Martinez <[hidden email]> wrote:

Dear Arek,

       First we would like to thank you for Biomart, is a fantastic tool for non-experts.
We have a huge dataset (Chipseq data) mapped on an older version of the zebrafish genome (zv8) and we would like to link it to some BIomart data, which works only with zv9. Currently Biomart can transform the GENOMIC POSITIONS  of genes annotated in zv8 to zv9, but NOT conversely.

       We would appreciate any suggestions to go around this problem without loosing too many data.

Thanks a lot in advance for your help,

Juan


Juan Ramón Martínez Morales
Centro Andaluz de Biología del Desarrollo (CABD)
(Andalusian Centre for Developmental Biology)
CSIC-Universidad Pablo de Olavide
Carretera de Utrera, Km1
41013 Sevilla, Spain
<a href="tel:%2B34954977827" value="+34954977827">+34954977827
[hidden email]








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Re: [BioMart Users] Request

Arek Kasprzyk
In reply to this post by Juan Martinez
Hi Juan,
I don't think BioMart can generate these positions. The genomic positions and other attributes of the zv9 gene set were included in this set that was loaded to the BioMart database. If you are running your own instance of BioMart then the simple remedy to your problem would to be to simply load older zv8 gene set instead. If you are talking about public BioMart instance that you are using then I would direct you to Ensembl archives where you can find previous versions of the genome including zv8

let me know if you need more help
a

On Fri, Sep 16, 2011 at 8:25 AM, Juan Martinez <[hidden email]> wrote:
Dear Arek,

Thanks a lot for the fast reply! Now we realize that our problem is something that may be beyond Biomart. What we have is a list of genes (with ensembl ID, corrsponding to the zv9 version of the genome). Currently, Biomart can generate an automatic list of attributes from these identifiers that can include Gene start and Gene End positions. The point is that these positions refer to the zv9 version of the genome... Can you see an easy way to obtain the equivalent positions from the zv8 version of the zebrafish genome?

Maybe this is a trivial issue for someone with a bioinformatics background, but that is the beauty of Biomart... even a biologist can use it.

Cheers,

Juan

Juan Ramón Martínez Morales
Centro Andaluz de Biología del Desarrollo (CABD)
(Andalusian Centre for Developmental Biology)
CSIC-Universidad Pablo de Olavide
Carretera de Utrera, Km1
41013 Sevilla, Spain
<a href="tel:%2B34954977827" value="+34954977827" target="_blank">+34954977827






On 16/09/2011, at 14:06, Arek Kasprzyk wrote:

Hi Juan,
could you elaborate more on BioMart 'translating genomic positions' of genes from zv8 to zv9?
I am unclear what you mean by that


cheers,
a



On Fri, Sep 16, 2011 at 6:53 AM, Juan Martinez <[hidden email]> wrote:

Dear Arek,

       First we would like to thank you for Biomart, is a fantastic tool for non-experts.
We have a huge dataset (Chipseq data) mapped on an older version of the zebrafish genome (zv8) and we would like to link it to some BIomart data, which works only with zv9. Currently Biomart can transform the GENOMIC POSITIONS  of genes annotated in zv8 to zv9, but NOT conversely.

       We would appreciate any suggestions to go around this problem without loosing too many data.

Thanks a lot in advance for your help,

Juan


Juan Ramón Martínez Morales
Centro Andaluz de Biología del Desarrollo (CABD)
(Andalusian Centre for Developmental Biology)
CSIC-Universidad Pablo de Olavide
Carretera de Utrera, Km1
41013 Sevilla, Spain
<a href="tel:%2B34954977827" value="+34954977827" target="_blank">+34954977827
[hidden email]










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Re: [BioMart Users] Request

Elena Rivkin
In reply to this post by Juan Martinez
Hi Juan,

You can try your query here:

http://aug2010.archive.ensembl.org/biomart/martview/

Its an archived version of ensembl mart containing version zv8

All the best,


Elena Rivkin, PhD
Outreach and Training Coordinator, Informatics and Bio-computing

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Tel: 647-258-4316
Toll-free: 1-866-678-6427
www.oicr.on.ca

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On 11-09-16 6:53 AM, "Juan Martinez" <[hidden email]> wrote:

>
>Dear Arek,
>
> First we would like to thank you for Biomart, is a fantastic tool for
>non-experts.
>We have a huge dataset (Chipseq data) mapped on an older version of the
>zebrafish genome (zv8) and we would like to link it to some BIomart data,
>which works only with zv9. Currently Biomart can transform the GENOMIC
>POSITIONS  of genes annotated in zv8 to zv9, but NOT conversely.
>
> We would appreciate any suggestions to go around this problem without
>loosing too many data.
>
>Thanks a lot in advance for your help,
>
>Juan
>
>
>Juan Ramón Martínez Morales
>Centro Andaluz de Biología del Desarrollo (CABD)
>(Andalusian Centre for Developmental Biology)
>CSIC-Universidad Pablo de Olavide
>Carretera de Utrera, Km1
>41013 Sevilla, Spain
>+34954977827
>[hidden email]
>
>
>
>
>
>
>_______________________________________________
>Users mailing list
>[hidden email]
>https://lists.biomart.org/mailman/listinfo/users

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users