Update readme.md

readme.md

@@ -27,6 +27,9 @@ The \*.sh file mentioned in this section is located under <a href="https://githu
 # 2 Prediction
 - Additionally adjust configuration parameters in files, *config_testing_cn_true.txt*, *config_normal_cn_true.txt*, *config_tumor_cn_true.txt* located at at the <a href="https://github.com/DIDSR/HPC_DPAI"> root </a> directory of the codes.
 - Run commands listed in the below subsections to launch SGE jobs to generate prediction matrices.
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+The \*.sh files mentioned in sections 2.1 and 2.2  below are located under <a href="https://github.com/DIDSR/HPC_DPAI/tree/master/prediction">prediction</a> directory while the config_*.txt files are at the <a href="https://github.com/DIDSR/HPC_DPAI"> root </a> directory of the codes.
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 ## 2.1 With color normalization
 - qsub process_main.sh ./config_testing_cn_true.txt  
 -- *process_main.sh* in turn submits a number of SGE jobs using *process_array.sh* which in turn runs *process_images_grp_normalization_wli.py* in the array jobs generated for every slide. Number of tasks in an array job determined automatically based on the number of groups in the corresponding HDF5 file.
@@ -38,7 +41,6 @@ The \*.sh file mentioned in this section is located under <a href="https://githu
 - qsub process_main.sh ./config_normal.txt  
 - qsub process_main.sh ./config_tumor.txt  
 
-The \*.sh files mentioned in sections 2.1 and 2.2  are located under <a href="https://github.com/DIDSR/HPC_DPAI/tree/master/prediction">prediction</a> directory while the config_*.txt files are at the <a href="https://github.com/DIDSR/HPC_DPAI"> root </a> directory of the codes.
 # 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 example run:  
 - qsub heatmap_main.sh test /scratch/mikem/UserSupport/weizhe.li/runs_process_cn_True/testing_wnorm_448_400_7690953