Update readme.md

readme.md

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 [3 Heatmap stitching](#3-heatmap-stitching)  
 [4 Retreiving run-time statistics](#4-Retreiving-run-time-statistics)  
 
+
 # 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 table for every HDF5 file. 
+- 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*.
+- 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. 
 ## 1.1 With color normalization
 - qsub split_main.sh ./config_testing_cn_true.txt  
 - qsub split_main.sh ./config_normal_cn_true.txt