| 71 | | This command will perform BAFsegmentation on the samples in the BAFsegmentation subdirectory ''extracted'' that are specified in the file ''sample_names.txt''. If you want to perform BAFsegmentation on a subset of samples you can edit ''sample_names.txt'' accordingly. The segmented data is stored in the BAFsegmentation subdirectory ''segmented''. |
| | 71 | This command will perform BAFsegmentation on the samples in the BAFsegmentation subdirectory ''extracted'' that are specified in the file ''sample_names.txt''. If you want to perform BAFsegmentation on a subset of samples you can edit ''sample_names.txt'' accordingly. |
| | 72 | |
| | 73 | |
| | 74 | BAFsegmentation can be run with different settings. To get an overview of parameters run BAFsegmentation with the following command: |
| | 75 | |
| | 76 | {{{ |
| | 77 | perl BAF_segment_samples.pl --help |
| | 78 | }}} |
| | 79 | |
| | 80 | ''Results'' |
| | 81 | |
| | 82 | 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. |
| | 83 | |
| | 84 | 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. |
