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

Timestamp:

Oct 17, 2008, 4:48:42 PM (16 years ago)

Author:

markus

Comment:

--

se.lu.onk.BAFsegmentation

@@ -39 +39 @@
 
 ''Recommendations''
- For Infinium data, we recommend using BAFsegmentation with data normalized using 
+ 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.
 
 ''Requirements''
@@ -96 +96 @@
   }}}
 
+  To run BAFsegmentation on data normalized with tQN use the following command:
+
+  {{{
+     perl BAF_segment_samples.pl --input_directory=path/to/tQN/normalized
+  }}}
+  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.
+
 ''Results''
 
   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.
 
-  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.
+  In the BAFsegmentation subdirectory ''plots'', the following postscript files are generated:
+    * 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.
+    * 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.
+    * A file with a plot for each chromosome of regions of allelic imbalance across all assays.
 
 === Contact ===