Hi, Libia. To answer your first question, the output from your intersection should look something like this:
chrX 151121598 151121608 lod=18 276 chrX 151121610 151121616 lod=17 270 chrX 151121650 151121659 lod=18 276 chrX 151121674 151121731 lod=82 451 The last column of data is your log odds score. For an explanation of table data, you can always click the "describe table schema" button in the Table Browser. To answer your second question, there is no more efficient way to acquire a conservation number. On the Intersection page, you might experiment with your overlap options to manage the number of results you get based on your requirements. In your previous post, you had mentioned putting this data into Excel. Excel has functions to generate statistics from the data you generate, but to advise you on the best way to do that would be outside the scope of this forum. 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: Thursday, October 13, 2011 9:17 AM To: [email protected] Subject: [Genome] Fwd: Log odds score for any conserved element in a gene 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
