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


Ignore:
Timestamp:
Jun 2, 2008, 2:14:53 PM (13 years ago)
Author:
markus
Comment:

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  • se.lu.onk.IlluminaSNPNormalization

    v3 v4  
    99=== License ===
    1010The tQN software is available as a stand-alone software package, and will become available as
    11 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].
     11as 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].
    1212
    1313=== Download tQN ===
     14
     15The software will be made available when the manuscript describing the method is accepted for publication.
    1416
    1517=== How to use tQN ===
     
    1921
    2022''Input data format''
    21   tQN is applied to data exported from !BeadStudio.
     23  tQN is applied to data exported from !BeadStudio. For a set of samples, the file should be tab-delimited in the following format:
     24  ||Name||Chr||Position||sample1.X||sample1.Y||sample2.X||sample2.Y||sample3.X||sample3.Y|| 
     25  ||rs12354060||1||10004||0.04424883||1.818238||0.03157751||1.632767||0.04973672||1.770216||
     26  ||rs2691310||1||46844||0.7046126||1.305445||0.8322142||1.271329||0.8042333||1.151523||
     27  ||...||...||...||...||...||...||...||...||...||
    2228
    23 ''Running the program''
     29  The data extracted from !BeadStudio needs to split into a separate file for each sample using the script ''split_beadstudio_samples.pl''
     30
     31  {{{ 
     32  ./split_beadstudio_samples.pl --beadstudio_file example/example_beadstudio_data.txt
     33  }}}
     34  where ''example_beadstudio_data.txt'' is a file exported from !BeadStudio in the format described above.
     35
     36  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.
     37
     38''Performing tQN''
     39
     40  Run tQN with the following command:
     41
     42  {{{ 
     43   ./tQN_normalize_samples.pl --beadchip=humancnv370-duo
     44  }}}
     45
     46  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:
     47
     48  {{{ 
     49   ./tQN_normalize_samples.pl --beadchip=humancnv370-duo --output_format=PennCNV
     50  }}}
     51
     52  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.
     53   
     54
     55
    2456
    2557=== Contact ===