Hello Martin, This issue is also currently being discussed by TCGA so regrettably, we can't provide conclusive advice at this time. Note that as you mention liftovers are available in both directions between hg18 and hg19 on the website (http://genome.ucsc.edu/cgi-bin/hgLiftOver) as well as in the form of a standalone utility (http://hgdownload.cse.ucsc.edu/admin/exe/).
Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 11/2/10 9:39 AM, Martin Jadersten wrote: > Hi! > > We are starting up a project were we plan to study hematological malignancies > with exome-seq. We are having a hard time to decide whether to analyze > against hg19 or hg18. The ongoing TCGA cancer sequencing project is analyzed > against hg18 as far as I have heard. This will no doubt generate a lot of > valuable data which can be used for comparisons. There are also more > annotations for hg18. > > I now it should be possible to lift over coordinates from hg19 to hg18 or the > other way around. Considering our project that will run during the coming > year, would you recommend to go for hg19? > > Best regards, > > Martin > > ********************************** > Martin Jädersten MD PhD > Post doc research fellow > Genome Sciences Centre, Aly Karsan lab > BC Cancer Research Centre, 9th floor > 675 West 10th Avenue > Vancouver, BC > V5Z 1L3 > Canada > > Phone (office): +1-604-675 70 34 > Phone (cell) +1-604-366 31 49 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
