http://www.goldenhelix.com/kb en-us http://www.goldenhelix.com/kb ActiveKB NX jlforsythe@goldenhelix.com Fri, 03 Sep 2010 02:47:48 MDT 20 http://www.goldenhelix.com/kb/questions/15/ http://www.goldenhelix.com/kb/questions/15/ <File 'try31807_30004_Xba.brlmm.cn.wig' - track load error:Limit of 10,000,000 length specification for bed format at line 1, found: 69250877> This error message is a result of certain re ... Josh Forsythe Wed, 16 Jan 2008 22:06:04 GMT http://www.goldenhelix.com/kb/questions/60/ http://www.goldenhelix.com/kb/questions/60/ When performing univariate segmenting analysis in CNAM, the results may contain segments that are only one marker in length. The UCSC Genome Browser does not accept data files containing segments ... Josh Forsythe Thu, 13 Mar 2008 22:58:42 GMT http://www.goldenhelix.com/kb/questions/65/ http://www.goldenhelix.com/kb/questions/65/ Using Illumina’s BeadStudio software you can create a marker map containing the SNPs, Chromosome and Physical Position pertaining your particular dataset under study. To generate the marker ma ... Josh Forsythe Fri, 14 Mar 2008 15:30:49 GMT http://www.goldenhelix.com/kb/questions/40/ http://www.goldenhelix.com/kb/questions/40/ This definition of FBAT-PC is courtesy of Jessica Lasky-Su from the following publication:Lasky-Su J, Faraone SV, Lange C, Biederman J, Tsuang M, Doyle AE, Smoller J, Laird N, Sklar P. Family base ... Josh Forsythe Tue, 25 Mar 2008 22:31:57 GMT http://www.goldenhelix.com/kb/questions/71/ http://www.goldenhelix.com/kb/questions/71/ In Golden Helix SVS 6.3 there is an option under the PBAT Test Statistic and Computational tab to output "signed" p-values for SNP, haplotype and copy number analysis (Figure 1). Choosing this opt ... Josh Forsythe Fri, 02 May 2008 00:15:16 GMT http://www.goldenhelix.com/kb/questions/10/ http://www.goldenhelix.com/kb/questions/10/ The first row of the PBAT pedigree file contains the names of the markers. Each subsequent row stands for one individual/subject, starting with the pedigree id. The pedigree id is a unique alphanu ... Josh Forsythe Wed, 16 Jan 2008 20:31:45 GMT http://www.goldenhelix.com/kb/questions/35/ http://www.goldenhelix.com/kb/questions/35/ We are really not sure if there are accepted rules of thumb, so a more cautious answer is, that it depends. There are certain population structures where large departures from HWE are legitimate, ... Josh Forsythe Thu, 17 Jan 2008 20:06:37 GMT http://www.goldenhelix.com/kb/questions/57/ http://www.goldenhelix.com/kb/questions/57/ The technique implemented in HelixTree to correct input data for population stratification by principal component analysis is based on the program EIGENSTRAT with a few enhancements. This techniq ... Josh Forsythe Tue, 19 Feb 2008 19:59:15 GMT http://www.goldenhelix.com/kb/questions/21/ http://www.goldenhelix.com/kb/questions/21/ Suppose that the SNP we are looking at has 2 alleles, A and B Select allele A to model. The following is true: 1. A recessive model is coded as 1 for the homozygous AA genotype and 0 otherwise ... Josh Forsythe Wed, 16 Jan 2008 23:24:39 GMT http://www.goldenhelix.com/kb/questions/30/ http://www.goldenhelix.com/kb/questions/30/ From the HelixTree Manual:The Correlation Interaction ViewThe figure aboveshows a matrix of the selected variables in the order they were sorted in the Multitree Model window. The numbers appearin ... Josh Forsythe Thu, 10 Apr 2008 17:05:01 GMT