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
