Category » Copy Number Analysis

There were 8 articles found in this category:

1. Tutorial: Whole Genome Copy Number Association Workflow
   http://www.goldenhelix.com/SNP_Variation/tutorials/cnv/introduction.html
2. Error: The copy number probe and SNP files do not have the same number of patients in them
   This error occurs when you're trying to process Affymetrix 5.0 and 6.0 CEL files for copy number analysis and the proper library files (with a *.cdf extension) have not been selected. The newest Affymetrix library files contain both SNP and CNV probes. Previous versions only contained SNP probes ...
3. Tutorial: How to Visualize Copy Number Analysis Segments and LogRs in Affymetrix’s GTC Browser
   Affymetrix provides a robust genome browser with its Genotyping Console software that enables you to visualize log2 ratios (referred to as LogRs) and copy number variations (CNVs) for each sample in your dataset. This tutorial will lead you step-by-step through exporting CNV segments and LogRs ...
4. Tutorial: How to Visualize LogRs and Segments in HelixTree
   In various live webinars and on our website, we have shown images similar to the one below, plotting each marker for a given sample vs. its mean log2 ratio (LogRs) and displaying visually how CNAM (actually HelixTree in this case) made the split (denoted by vertical magenta lines). There is not ...
5. Speeding up Copy Number Analysis
   Copy Number Segmentation can take a considerable time especially on Affymetrix 6.0 and Illumina 1M data. There are few options we suggest to speed things up: CNAM can take advantage of multi-core and multi-processor machines. If you have a multi-core machine, we suggest matching the number of t ...
6. Message error importing UCSC Wiggle Format - segment is only one marker in length
   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 with length equal to one. To avoid this conflict, set the Min #Markers per segment parameter in the ...
7. Importing Affymetrix 5.0 and 6.0 marker maps (annotation files) for Copy Number Analysis
   Affymetrix 5.0 and 6.0 annotation files come in two separate files, one containing SNP probes and the other copy number probes. In order to properly process and analyze 5.0 and 6.0 data for copy number analysis you need the set merged and imported into HelixTree. HelixTree makes this easy usin ...
8. Message error importing UCSC Wiggle Format - segment spans distance greater than 10,000,000 base pairs
   <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 restrictions that UCSC has for its online genome browser. This particular restriction requires that no ...