Changes between Version 3 and Version 4 of se.lu.onk.IlluminaSNPNormalization

Timestamp:

Jun 2, 2008, 2:14:53 PM (17 years ago)

Author:

markus

Comment:

--

se.lu.onk.IlluminaSNPNormalization

@@ -9 +9 @@
 === License ===
 The tQN software is available as a stand-alone software package, and will become available as
-as a plug-in to BASE as the handling of SNP arrays in BASE is developed. Both versions under the [http://www.gnu.org/copyleft/gpl.html GNU General Public License].
+as a plug-in to BASE as the handling of SNP arrays in BASE is developed. Both versions are available under the [http://www.gnu.org/copyleft/gpl.html GNU General Public License].
 
 === Download tQN ===
+
+The software will be made available when the manuscript describing the method is accepted for publication.
 
 === How to use tQN ===
@@ -19 +21 @@
 
 ''Input data format''
-  tQN is applied to data exported from !BeadStudio.
+  tQN is applied to data exported from !BeadStudio. For a set of samples, the file should be tab-delimited in the following format:
+  ||Name||Chr||Position||sample1.X||sample1.Y||sample2.X||sample2.Y||sample3.X||sample3.Y||  
+  ||rs12354060||1||10004||0.04424883||1.818238||0.03157751||1.632767||0.04973672||1.770216||
+  ||rs2691310||1||46844||0.7046126||1.305445||0.8322142||1.271329||0.8042333||1.151523||
+  ||...||...||...||...||...||...||...||...||...||
 
-''Running the program''
+  The data extracted from !BeadStudio needs to split into a separate file for each sample using the script ''split_beadstudio_samples.pl''
+
+  {{{  
+  ./split_beadstudio_samples.pl --beadstudio_file example/example_beadstudio_data.txt
+  }}}
+  where ''example_beadstudio_data.txt'' is a file exported from !BeadStudio in the format described above.
+
+  This script will generate one file per sample together with a file ''sample_names.txt'' in the tQN subdirectory ''extracted''. These files are used when tQN is run and can be deleted once the samples are normalized.
+
+''Performing tQN''
+
+  Run tQN with the following command:
+
+  {{{  
+   ./tQN_normalize_samples.pl --beadchip=humancnv370-duo
+  }}}
+
+  This command will perform tQN on the samples in the tQN subdirectory ''extracted'' that are specified in the file ''sample_names.txt''. If you want to perform tQN on a subset of samples you can edit ''sample_names.txt'' accordingly. The normalized data is stored in the tQN subdirectory ''normalized''. For each sample, there is a file with tQN normalized data. A file ''tQN_beadstudio.txt'' is also generated with tQN BAF and Log R Ratios for all samples in a format suitable for import into !BeadStudio using its import column process. tQN also supports generating tQN data for further analysis with PennCNV and QuantiSNP. Running tQN with the following command:
+
+  {{{  
+   ./tQN_normalize_samples.pl --beadchip=humancnv370-duo --output_format=PennCNV
+  }}}
+
+  generates one data file per sample in the tQN subdirectory ''normalized'' for further analysis using PennCNV. Alternatives for ''--output_format'' are ''QuantiSNP'', which generates one data file per sample for further analysis with QuantiSNP and ''!BeadStudio'', which is the default argument generating the default ''tQN_beadstudio.txt'' file with data for all samples.
+   
+
+
 
 === Contact ===