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@@ -6,17 +6,17 @@
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# 1 Image patch extract
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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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-## Without color normalization
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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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-## With color normalization
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+## 1.2 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.txt
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qsub split_main.sh ./config_tumor.txt
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-## Creating lookup tables
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+## 1.3 Creating lookup tables
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bash create_lookup_grp.sh ./config_testing.txt
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bash create_lookup_grp.sh ./config_normal.txt
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bash create_lookup_grp.sh ./config_tumor.txt
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@@ -24,38 +24,21 @@ bash create_lookup_grp.sh ./config_tumor.txt
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The lookup tables are created only once.
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# 2 Prediction
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-
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-# 3 Heatmap stitching
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-
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-
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-qsub heatmap_main.sh test /scratch/mikem/UserSupport/weizhe.li/runs_process_cn_True/testing_wnorm_448_400_7690953
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-
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-# For color normalization True
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+The following commands launch Son of SGE jobs to generate prediction matrices.
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+## 2.1 With color normalization
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qsub process_main.sh ./config_testing_cn_true.txt
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qsub process_main.sh ./config_normal_cn_true.txt
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qsub process_main.sh ./config_tumor_cn_true.txt
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-# For color normalization False
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-* qsub process_main.sh ./config_testing.txt
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-qsub process_main.sh ./config_normal.txt
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-qsub process_main.sh ./config_tumor.txt
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-
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-
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-qsub split_main.sh ./config_testing.txt
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-bash create_lookup_grp.sh ./config_testing.txt
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+## 2.2 Without color normalization
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qsub process_main.sh ./config_testing.txt
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-
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-qsub split_main.sh ./config_normal.txt
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-bash create_lookup_grp.sh ./config_normal.txt
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qsub process_main.sh ./config_normal.txt
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-
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-qsub split_main.sh ./config_tumor.txt
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-bash create_lookup_grp.sh ./config_tumor.txt
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qsub process_main.sh ./config_tumor.txt
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-#Real Cool Heading
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+# 3 Heatmap stitching
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+After the predictions matrices have been generated the following SGE job could be launched to genertae heatmaps.
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+qsub heatmap_main.sh test /scratch/mikem/UserSupport/weizhe.li/runs_process_cn_True/testing_wnorm_448_400_7690953
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-qsub split_main.sh ./config_testing_wc.txt
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# TESTING
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Mike Mikailov