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=ENSMUSG000000 26349;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 > > > 129670740,129671677,129688181,129689934,129691831,129694417,12969596 6,129698182,129698738, > > > > exonEnds exonCount > > 980 > > > 129670962,129671759,129688310,129689995,129691894,129694463,12969613 0,129698253,129701414, > > 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.mskc="" c.org="" %7elianos="" contact=""> > -- Sabrina [[alternative HTML version deleted]]