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

Timestamp:

Jun 1, 2010, 3:43:33 PM (14 years ago)

Author:

markus

Comment:

--

se.lu.onk.BAFsegmentation

@@ -11 +11 @@
 === News ===
 
- * Jun. 1, 2010. BAFsegmentation 1.2.0 release. Added support for paired tumor-normal samples. 
+ * Jun. 1, 2010. BAFsegmentation 1.2.0 release. Added support for analysing paired tumor-normal samples. 
 
  * 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.
@@ -108 +108 @@
 
 
-  __Mixing paired and unpaired samples__
-
 ''Performing BAFsegmentation''
 
@@ -134 +132 @@
   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.
 
+  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:
+
+  ||!FilenameAssay||!FilenameNormal||
+  ||Sample1_extracted.txt||Normal1_extracted.txt||
+  ||Sample2_extracted.txt||Normal2_extracted.txt||
+  || ... || ... ||
+
+  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.
+
 ''Results''