Changes between Version 14 and Version 15 of se.lu.onk.BAFsegmentation


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Timestamp:
Sep 17, 2008, 12:50:08 PM (14 years ago)
Author:
markus
Comment:

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  • se.lu.onk.BAFsegmentation

    v14 v15  
    1414=== Download BAFsegmentation ===
    1515
    16 The method will be downloadable as a stand-alone version soon.
     16[http://cbbp.thep.lu.se/~markus/software/BAFsegmentation/BAFsegmentation-1.0.0.zip?format=raw Download the latest stand-alone release (BAFsegmentation 1.0.0)]
    1717
    1818=== Supplemental Data ===
     
    4646
    4747''Input data format''
    48   BAFsegmentation is applied to data exported from !BeadStudio. For a set of samples, the file exported from !BeadStudio should be tab-delimited in the following format:
     48  BAFsegmentation is applied to data for a set of samples in a file that should be tab-delimited in the following format:
    4949  ||Name||Chr||Position||sample1.B Allele Freq||sample1.Log R Ratio||sample2.B Allele Freq||sample2.Log R Ratio||sample3.B Allele Freq||sample3.Log R Ratio||...||
    5050  ||rs12354060||1||10004||1||0.110391||1||-0.05188531||1||0.07706165||...||
     
    5252  ||...||...||...||...||...||...||...||...||...||...||
    5353
    54   The data extracted from !BeadStudio needs to be split into a separate file for each sample using the script ''split_beadstudio_samples.pl''.
     54  For Illumina arrays data can be exported in this format directly from !BeadStudio. The data need to be split into a separate file for each sample using the script ''split_samples.pl''.
    5555
    5656  {{{ 
    57     perl split_beadstudio_samples.pl --beadstudio_file=example/example_beadstudio_data.txt
     57    perl split_samples.pl --data_file=example/example_beadstudio_data.txt
    5858  }}}
    5959  where ''example_beadstudio_data.txt'' is a file exported from !BeadStudio in the format described above.