Dear All, I would like to know the difference between ensembl genes and refseq genes. i would appreciate if any one can tell me what is the average intergenic distance in both human and mouse?? Any help is appreciated. Chris. [[alternative HTML version deleted]]

On Thu, Mar 15, 2012 at 1:50 AM, chris Jhon <cjhon217 at="" gmail.com=""> wrote: > Dear All, > > > I would like to know the difference between ensembl genes and refseq genes. > i would appreciate if any one can tell me what is the average intergenic > distance in both human and mouse?? Hi, Chris. You might take a look at the rtracklayer package to get the refGene and ensgene tracks for human and mouse from UCSC. Sean

Hi Chris, On Thursday, March 15, 2012, chris Jhon <cjhon217@gmail.com> wrote: > Dear All, > > > I would like to know the difference between ensembl genes and refseq genes. Refseq annos tend to be more conservative -- I'm not sure how many of them are computationally predicted vs. ensembl, for instance. > i would appreciate if any one can tell me what is the average intergenic > distance in both human and mouse?? If I gave you a number, would you believe me? :-) This is something you can hash out yourself if you get a bit familiar with IRanges and GenomicRanges functionality -- then whip up a GenomicFeatures TranscriptDb for your two organisms and have a crack at it. After you do that, report back here with your best guess and the code you used to get it ... I'll offer up mine then, too ;-) -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 [[alternative HTML version deleted]]