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@@ -3,8 +3,10 @@
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[3 Heatmap stitching](#3-heatmap-stitching)
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[4 Retreiving run-time statistics](#4-Retreiving-run-time-statistics)
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+
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# 1 Image patch extraction
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-The following commands launch Son of Grid Engine (SGE) jobs to extract, group patches in HDF5 files and create a lookup table for every HDF5 file.
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+- Adjust configuration parameters in files, *config_testing_cn_true.txt*, *config_normal_cn_true.txt*, *config_tumor_cn_true.txt*, *config_testing.txt*, *config_normal.txt* and *config_tumor.txt*.
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+- Run the following commands to launch Son of Grid Engine (SGE) jobs to extract, group patches in HDF5 files and create a lookup table for every HDF5 file.
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## 1.1 With color normalization
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- qsub split_main.sh ./config_testing_cn_true.txt
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- qsub split_main.sh ./config_normal_cn_true.txt
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Mike Mikailov