[BioC] how to get gene information?

[Sean Davis]

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