Steve, Thank you for your quick response!
So when I intersect the conservation table with the USCS genes, what part of that new table is related to conservation? I do not understand. I was wondering if there was a more efficient way to acquire a conservation number related to each gene (sum of logs, average, or something similar) that is a bit less complicated? After trying what you mentioned I saw that each gene has hundreds of log scores, making this a bit difficult. Thanks agan, Libia On Oct 12, 2011 2:51 PM, "Steve Heitner" <[email protected]> wrote: > 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
