I am analyzing Affy SNP6 array data for CNVs and would like to use GenomeBrowse to visualize the LRR and BAF for each chromosome.
Is there a way to visualize the LRR and BAF for each chromosome in Golden Helix or GenomeBrowse directly from the .cel files? If not, how do I convert my .cel files into the bam, bed or vcf file format for GenomeBrowse?
Dear Elizabeth,
Since Affymetrix CEL files are binary files specific to the array that provide the data GenomeBrowse is unable to read the LRR and BAF data for visualization directly from the CEL files.
Additionally GenomeBrowse does not currently support numeric value type plots, we are in the process of adding that functionality so that numeric value columns from inside of supported file formats (ex. Read Depths and Quality Scores from VCF files) can be visualized along with the standard variant and coverage files the are currently drawn, this functionality should be available within the next few months.
However, our commercial analysis software SVS can import the CEL file data (LRR and BAF) directly into spreadsheets which can then be plotted on a genomic scale so you can visualized the data per chromosome for each one of your samples (either together or separately). You can find specifics on importing this file type in our SVS Manual.
Please let me know if you have any further questions.
Thanks, Jami...
Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.
Asked: 2013-11-15 09:26:02 -0600
Seen: 407 times
Last updated: Nov 15 '13
