Hi Santi and Max, Thanks for pointing this out. Max, I think you are right -- the annotations are for hg17 but the links are for hg19. I will forward this email thread to [email protected] (listed on the contacts page).
-- Brooke Rhead UCSC Genome Bioinformatics Group On 11/23/10 09:50, Maximilian Haussler wrote: > I can confirm and add something to Santi's bug report, as I've seen this > before in my files as well. > > The last version of the enhancer browser annotation was on hg17. > If you take the the current hg19 coordinates and lift them them from hg17 to > hg19, then they are correct. The download file from the enhancer browser > might have been on hg17 although they had already switched to hg19 for their > website, but I am not sure about this. > > best, > Max > > > On Mon, Nov 22, 2010 at 4:13 PM, sgonzal <[email protected]> wrote: > >> I am writting this email to inform you about the incorrect annotation of >> your "enhancer browser" in your genome browser. >> >> As easy as look any of the validated enhancer that USCS shows in genome >> browser and consulting the outsite information about that enhancer to check >> that the position is absolutly wrong. Just need to copy the experimentally >> validated region and run a BLAT to check that the region that genome >> browser shows does not correspond with the descrived one. >> >> One easy example, but all the annotation is wrong: >> >> UCSC genome browser: >> >> http://genome.ucsc.edu/cgi-bin/hgTracks?insideX=136&revCmplDisp=0&hgsid=173058138&hgt_doJsCommand=&position=chr16%3A84%2C982%2C748-84%2C999%2C968&hgtgroup_user_close=0&hgtgroup_map_close=0&hgtgroup_phenDis_close=1&hgtgroup_genes_close=0&hgtgroup_rna_close=0&hgtgroup_expression_close=0&hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_varRep_close=0 >> >> Outlink annotation of the enhancer: >> >> http://enhancer-test.lbl.gov/cgi-bin/imagedb3.pl?form=presentation&show=1&organism_id=1&experiment_id=element_1 >> >> Correct enhancer position shown by BLAT: >> >> http://genome.ucsc.edu/cgi-bin/hgTracks?insideX=136&revCmplDisp=0&hgsid=173058354&hgt_doJsCommand=&hgt.out3=10x&position=chr16%3A86430087-86430726&hgtgroup_user_close=0&hgtgroup_map_close=0&hgtgroup_phenDis_close=1&hgtgroup_genes_close=0&hgtgroup_rna_close=0&hgtgroup_expression_close=0&hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_varRep_close=0 >> >> I hope it can help you to solve your problems, >> >> Santi. >> >> -- >> Santiago Gonzalez RosadoJUNIOR RESEARCHER >> Life Sciences - Computational Genomics >> Barcelona Supercomputing Center (BSC) >> Centro Nacional de Supercomputacion (CNS) >> Nexus II - Planta 1 >> C/ JORDI GIRONA, 29, 08034 Barcelona >> >> WARNING / LEGAL TEXT: This message is intended only for the use of the >> individual or entity to which it is addressed and may contain >> information which is privileged, confidential, proprietary, or exempt >> from disclosure under applicable law. If you are not the intended >> recipient or the person responsible for delivering the message to the >> intended recipient, you are strictly prohibited from disclosing, >> distributing, copying, or in any way using this message. If you have >> received this communication in error, please notify the sender and >> destroy and delete any copies you may have received. >> >> http://www.bsc.es/disclaimer.htm >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
