Hello Shay, You are correct, there is definitely gene annotation in your region in the hg18 assembly. However, I noticed that there is only EST data for the same region in hg19.
By any chance was the Table browser set to hg19 when you ran your queries? It is the default and easy to overlook. Other potential problems: region not set correctly, old filters in place, that type of thing. Doing a cart-reset (bottom on form) can help you to ensure that the query is starting-from-scratch. Note that a cart-reset will clear any custom tracks - so save them into a Session (if you have any) before doing this. Please let us know how things work after double checking with a cart-reset and the database set to hg18. Thanks, Jennifer ps: hg18 -> Human Mar. 2006 (NCBI36/hg18) Assembly hg19 -> Human Feb. 2009 (GRCh37/hg19) Assembly --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/3/10 4:17 AM, Shay Tzur wrote: > Hello! > > I was working with the genome browser and looked on specific region in > chromosome 22 that contains four well known genes (with gene_id and NCBI > references) . However, when I tried to download their coordinates or their > exonic coordinates with the Table tool (BED file). I noticed that they are > not exist in the table. I used other tables as well but the data in this > region was still missing. I don't understand how can it be , since you can > see the genes in the browser but not in tables? > > I will be happy to get you help please, > > the region is in chr22 between 34500000-35000000 (asse. 36). > > > Best regards, > > Shay Tzur > The Technion, > Israel > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
