Changes between Version 25 and Version 26 of se.lu.onk.BAFsegmentation


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Timestamp:
Oct 17, 2008, 4:48:42 PM (9 years ago)
Author:
markus
Comment:

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  • se.lu.onk.BAFsegmentation

    v25 v26  
    3939
    4040''Recommendations''
    41  For Infinium data, we recommend using BAFsegmentation with data normalized using
     41 For Infinium data, we recommend using BAFsegmentation with data normalized using [wiki:se.lu.onk.IlluminaSNPNormalization tQN]. BAFsegmentation benefits from the symmetrical B allele frequencies obtained with tQN.
    4242
    4343''Requirements''
     
    9696  }}}
    9797
     98  To run BAFsegmentation on data normalized with tQN use the following command:
     99
     100  {{{
     101     perl BAF_segment_samples.pl --input_directory=path/to/tQN/normalized
     102  }}}
     103  where ''path/to/tQN'' is the path to your tQN directory in which you have a directory ''normalized'' with your tQN normalized data. Note that tQN is used with X and Y intensities. Please look at [wiki:se.lu.onk.IlluminaSNPNormalization tQN] for further instructions on how to use tQN and prepare your data for use with tQN.
     104
    98105''Results''
    99106
    100107  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.
    101108
    102   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.
     109  In the BAFsegmentation subdirectory ''plots'', the following postscript files are generated:
     110    * A file for each sample with 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 with average log R ratios within mBAF segments superimposed.
     111    * A file for each sample with two plots for the whole genome: a plot with segmented mBAF and a plot with average log R ratios within mBAF segments.
     112    * A file with a plot for each chromosome of regions of allelic imbalance across all assays.
    103113
    104114=== Contact ===