Hi, Libia. Intersection results are always in terms of the first table, so if you're looking for information regarding conservation, you should start with the conservation table and then intersect it with UCSC Genes. When you create the intersection in this order, the last column will be the conservation score (log odds score).
As an aside, if you were using the identifiers function to define your genes/regions, you will now have to use the define regions button. Note that you can only define 1,000 regions this way - you will need to use a custom track if you have more genes than that. Please write back if you need assistance with this. 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 Libia Pava Sent: Tuesday, October 11, 2011 9:47 PM To: [email protected] Subject: [Genome] Log odds score for any conserved element in a gene Hello, I'm trying to collect the log odds score for any conserved element in a gene by intersecting two tables but I'm unable to get an actual log score. After selecting the chromosomal position of the genes I want I go to Tables. Then Under gene and Gene Prediction Tracks, UCSC Genes, I intersect the position I want with phastConsElements46wayPlacental, but the excel file I gather has no log odds scores. The BED table shows me the number of exons, the number of base pairs in each exon, and also some values which I'm unable to interpret that are related to the number of exons. Are these values the phastCon score presenting the exons of each gene? If so, why is the first number always 0? Is this the correct way of gathering the data I want (a conserve score for each gene), if so why am I not getting a score? If I'm doing this wrong I would appreciate any feedback on how to do it better. Thanks, Libia _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
