Changes between Version 13 and Version 14 of se.lu.onk.BAFsegmentation


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Timestamp:
Sep 17, 2008, 12:06:03 PM (14 years ago)
Author:
markus
Comment:

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  • se.lu.onk.BAFsegmentation

    v13 v14  
    6969  }}}
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    71   This command will perform BAFsegmentation on the samples in the BAFsegmentation subdirectory ''extracted'' that are specified in the file ''sample_names.txt''. If you want to perform BAFsegmentation on a subset of samples you can edit ''sample_names.txt'' accordingly. The segmented data is stored in the BAFsegmentation subdirectory ''segmented''.
     71  This command will perform BAFsegmentation on the samples in the BAFsegmentation subdirectory ''extracted'' that are specified in the file ''sample_names.txt''. If you want to perform BAFsegmentation on a subset of samples you can edit ''sample_names.txt'' accordingly.
     72
     73
     74  BAFsegmentation can be run with different settings. To get an overview of parameters run BAFsegmentation with the following command:
     75
     76  {{{ 
     77     perl BAF_segment_samples.pl --help
     78  }}}
     79
     80''Results''
     81
     82  The segmented regions identified as allelic imbalance are stored in the file ''AI_regions.txt'' in the BAFsegmentation subdirectory ''segmented''. In addition an xml-file ''AI_regions.xml'' with the regions is also produced. This xml-file can be imported as a bookmark file into the Illumina !BeadStudio software for visualization and further analysis of the identified regions.
     83
     84  In the BAFsegmentation subdirectory ''plots'', a postscript file is generated for each sample. These plot files contain three plots per chromosome: a BAF plot with non-informative homozygous SNPs removed, an mBAF plot with non-informative homozygous SNPs removed and with superimposed segmentation line, and a log R ratio plot with all SNPs.
    7285
    7386=== Contact ===