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@@ -5,13 +5,13 @@
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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 tables for every HDF5 file.
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-## 1.1 Without color normalization
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-qsub split_main.sh ./config_testing.txt
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-qsub split_main.sh ./config_normal.txt
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-qsub split_main.sh ./config_tumor.txt
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-
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-## 1.2 With color normalization
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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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+qsub split_main.sh ./config_tumor_cn_true.txt
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+
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+## 1.2 Without color normalization
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+qsub split_main.sh ./config_testing.txt
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qsub split_main.sh ./config_normal.txt
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qsub split_main.sh ./config_tumor.txt
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@@ -41,7 +41,7 @@ qsub heatmap_main.sh test /scratch/mikem/UserSupport/weizhe.li/runs_process_cn_T
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# 4 Retreiving run-time statistics
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In time_all_stats_pred.sh file adjust job results root directory, like:
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DIR=/scratch/mikem/UserSupport/weizhe.li/runs_process_cn_False/normal_wnorm_448_400_7691563
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-Then run:
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+Then run:
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time bash ./time_all_stats_pred.sh
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Mike Mikailov