Changes between Version 36 and Version 37 of se.lu.onk.BAFsegmentation


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Timestamp:
Jun 1, 2010, 3:43:33 PM (12 years ago)
Author:
markus
Comment:

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  • se.lu.onk.BAFsegmentation

    v36 v37  
    1111=== News ===
    1212
    13  * Jun. 1, 2010. BAFsegmentation 1.2.0 release. Added support for paired tumor-normal samples.
     13 * Jun. 1, 2010. BAFsegmentation 1.2.0 release. Added support for analysing paired tumor-normal samples.
    1414
    1515 * Mar. 13, 2009. BAFsegmentation 1.1.2 release. This is a minor bug-fix release. Fixed bugs include errors in documentation (default has never been to remove cnv probes), handling of when there are no probes for entire chromosomes, and 'split_samples.pl' can now handle language settings for which !BeadStudio generates files in which comma denotes the decimal point.
     
    108108
    109109
    110   __Mixing paired and unpaired samples__
    111 
    112110''Performing BAFsegmentation''
    113111
     
    134132  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.
    135133
     134  To run BAFsegmentation on paired tumor-normal samples a file named ''normal_sample_names.txt'' has to be created and put in the directory ''extracted''. The file ''normal_sample_names.txt'' should be tab-separated in the following format:
     135
     136  ||!FilenameAssay||!FilenameNormal||
     137  ||Sample1_extracted.txt||Normal1_extracted.txt||
     138  ||Sample2_extracted.txt||Normal2_extracted.txt||
     139  || ... || ... ||
     140
     141  This file allows to user to provide the required mapping between tumor-normal pairs. A single normal sample can be used for multiple tumor samples. It is also possible to mix analysis with paired and unpaired samples: samples not present in ''normal_sample_names.txt'' are analysed as unpaired tumor samples.
     142
    136143''Results''
    137144