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 <[email protected]> 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 > +34954977827 > [email protected] > > > > > > > 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 <[email protected]> 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 >> [email protected] >> >> >> >> >> >> >> > >
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