Hello, Glauber. No, you are not doing anything wrong. This is a question that has been asked on more than a few occasions. Please see the following previously-answered mailing list question: https://lists.soe.ucsc.edu/pipermail/genome/2009-June/019352.html
Regardless of the actual direction of transcription, exonStart and txStart will always be numerically smaller than or equal to exonEnd and txEnd in our tables, so it appears that the data contradicts what you are seeing, but this is by design. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Glauber Brito Sent: Tuesday, June 19, 2012 9:12 AM To: [email protected] Subject: [Genome] transcript genomic coordinates Dear colleague, I downloaded human RefSeq genomic coordinates using the Table Browser tool in order to identify bidirectional promoters. I checked some gene pairs known to be in head-to-head configuration (less than 1000 bp apart). Strangely a significant difference (~15-29 kb) was observed for these pairs according to my calculations, which were basically finding genes in the same chromosome and in opposite strands and having TSSs less than 1000 bp apart, without overlapping. In fact, the Genome Browser showed these genes as regulated by bidirectional promoters (head-to-head orientation), while the genomic coordinates didn't. I attached somes slides depicting some of these flaws. Am I doing something wrong? I appreciate your help. Cheers, Glauber ---------------------------------------------- Glauber C. Brito, PhD Centro de Investigação Translacional em Oncologia Instituto do Câncer do Estado de São Paulo Faculdade de Medicina da Universidade de São Paulo Av. Dr. Arnaldo, 251. Cerqueira César CEP 01246-000 - São Paulo - SP - Brasil Tel: + 55 11 38933007 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
