Hi, Steve:
Thanks! I never thought of that , because when I use UCSC online browser, it
gave the same coordinate as from Ensembl. Thanks for the info and I will
readjust my code!

Sabrina

On Thu, Mar 4, 2010 at 11:07 AM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi,
>
> On Thu, Mar 4, 2010 at 10:41 AM, sabrina s <sabrina.shao@gmail.com> wrote:
> > Hi, all
> > I don't know if it is just by chance, I was retrieving sequence for
> > ENSMUST00000027587<
> http://www.ensembl.org/Mus_musculus/Transcript/Exons?g=ENSMUSG00000026349;t=ENSMUST00000027587
> >using
> > BSgenome
> > the coordinate I use was what  I retrieved from UCSC through following
> code:
> >
> >  library(rtracklayer)
> >     session <- browserSession()
> >     genome(session) <- "mm9"
> >
> > q2<- ucscTableQuery(session,"
> > ensGene")
> > ensGene<-getTable(q2)
> >
> > the result is:
> >  name name2 chrom strand   txStart     txEnd
> > 980 NM_028399 Ccnt2  chr1      + 129670740 129701414
> >
> > exonStarts
> > 980
> >
> 129670740,129671677,129688181,129689934,129691831,129694417,129695966,129698182,129698738,
> >
> > exonEnds exonCount
> > 980
> >
> 129670962,129671759,129688310,129689995,129691894,129694463,129696130,129698253,129701414,
> > 9
> >
> >
> > But from Ensembl or even UCSC genome browser, the first exon coordinate
> > starts at  129670741, so there is 1 bp shift.
>
> Look at the description of how the "coordinates" work as supplied by UCSC:
>
> http://genome.ucsc.edu/FAQ/FAQtracks#tracks1
>
> > Because of that, I can't get
> > the right sequence that I need. So there is anyway to correct that or am
> I
> > missing some steps? Thanks!
>
> You can get what you need, you just hat to know when you need to add
> or subtract 1 from the start position.
>
> Hope that helps,
>
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact<http://cbio.mskcc.org/%7Elianos/contact>
>



-- 
Sabrina

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