Update readme.md

readme.md

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 # 1 Image patch extraction
 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. 
 ## 1.1 With color normalization
-qsub split_main.sh ./config_testing_cn_true.txt  
-qsub split_main.sh ./config_normal_cn_true.txt  
-qsub split_main.sh ./config_tumor_cn_true.txt  
+- qsub split_main.sh ./config_testing_cn_true.txt  
+- qsub split_main.sh ./config_normal_cn_true.txt  
+- qsub split_main.sh ./config_tumor_cn_true.txt  
 
 ## 1.2 Without color normalization
-qsub split_main.sh ./config_testing.txt  
-qsub split_main.sh ./config_normal.txt  
-qsub split_main.sh ./config_tumor.txt  
+- qsub split_main.sh ./config_testing.txt  
+- qsub split_main.sh ./config_normal.txt  
+- qsub split_main.sh ./config_tumor.txt  
 
 ## 1.3 Creating lookup tables
-bash create_lookup_grp.sh ./config_testing.txt  
-bash create_lookup_grp.sh ./config_normal.txt  
-bash create_lookup_grp.sh ./config_tumor.txt  
+- bash create_lookup_grp.sh ./config_testing.txt  
+- bash create_lookup_grp.sh ./config_normal.txt  
+- bash create_lookup_grp.sh ./config_tumor.txt  
 
 The lookup tables are created only once. 
 
 # 2 Prediction
 The following commands launch Son of SGE jobs to generate prediction matrices.
 ## 2.1 With color normalization
-qsub process_main.sh ./config_testing_cn_true.txt  
-qsub process_main.sh ./config_normal_cn_true.txt  
-qsub process_main.sh ./config_tumor_cn_true.txt  
+- qsub process_main.sh ./config_testing_cn_true.txt  
+- qsub process_main.sh ./config_normal_cn_true.txt  
+- qsub process_main.sh ./config_tumor_cn_true.txt  
 
 ## 2.2 Without color normalization 
-qsub process_main.sh ./config_testing.txt  
-qsub process_main.sh ./config_normal.txt  
-qsub process_main.sh ./config_tumor.txt  
+- qsub process_main.sh ./config_testing.txt  
+- qsub process_main.sh ./config_normal.txt  
+- qsub process_main.sh ./config_tumor.txt  
 
 # 3 Heatmap stitching
 After the predictions matrices have been generated an SGE job using heatmap_main.sh SGE scrip could be launched to genertae heatmaps. Two arguments for this launch are: a) type of the slides (test, normal or tumor); b) the root directory of the results, like in below ecxample run:  
-qsub heatmap_main.sh test /scratch/mikem/UserSupport/weizhe.li/runs_process_cn_True/testing_wnorm_448_400_7690953
+- qsub heatmap_main.sh test /scratch/mikem/UserSupport/weizhe.li/runs_process_cn_True/testing_wnorm_448_400_7690953
 
 # 4 Retreiving run-time statistics
 In time_all_stats_pred.sh file adjust job results root directory, like:  
-DIR=/scratch/mikem/UserSupport/weizhe.li/runs_process_cn_False/normal_wnorm_448_400_7691563  
+- DIR=/scratch/mikem/UserSupport/weizhe.li/runs_process_cn_False/normal_wnorm_448_400_7691563  
 Then run:  
-time bash ./time_all_stats_pred.sh  
+- time bash ./time_all_stats_pred.sh