Sean,

Thank you for your reply. I just realized that I can directly download the
information from UCSC.

Thanks.

-Roger

On 7/7/07, Sean Davis <sdavis2@mail.nih.gov> wrote:
> Roger Liu wrote:
> > Hi,
> >
> > I want to retrieve all the genes information from certain chromosome,
such
> > as Chr1. I would like to have the information like: gene transcription
start
> > site, end site, primary transcript start site and end site, exon start
site,
> > end site, and gene ID (gene bank accession #....).
> >
> > It seems that biomaRt can do this, but it can only give one set of start
> > site and end site (transcription start/end site, or primary start/end
site?
> > which one is right?)  and the ID is ensemble ID, I prefer to get
GeneBank
> > ID.
> >
> > Therefore, who know some packages or method can retrieve all the genes'
> > information from a chromosome,including gene transcription start site,
end
> > site, primary transcript start site and end site, exon start site, end
site,
> > and gene ID.
> >
>
> First, keep in mind that genes do not have starts and ends on the
> chromosome, technically.  Transcripts do.  So, if what you want is the
> mapping between transcripts and the genome, you can use biomart or you
> can download the tables below from the ucsc genome browser site (for
> human, build 36--would be similar links for other species, etc):
>
> http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/refFlat.txt.gz
>
> and
>
> http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/refLink.txt.gz
>
> Sean
>
>

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