StoHi-C (pronounced "stoic"): A stochastic Neighbor embedding approach for predicting 3D genome organization from Hi-C data.
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Example command line execution for StoHi-C:
------------------------ 999a WT ---------------------------
./stohic.sh data/999a_WT/GSM1379427.matrix step1/tSNE/results/999a_WT/pombeXYZ.txt step1/tSNE/results/999a_WT/pombeDIST.txt step2/results/plotly/999a_WT/pombe_999aWT.png step2/results/plotly/999a_WT/pombe_999aWT.html running step 1... tSNE runtime: 10.552345991134644 seconds running step 2... Step 2 runtime: 5.696078062057495 seconds
------------------------ G1-Arrested ------------------------
./stohic.sh data/G1-arrested/GSM1379429.matrix step1/tSNE/results/G1-arrested/pombeXYZ.txt step1/tSNE/results/G1-arrested/pombeDIST.txt step2/results/plotly/G1-arrested/pombe_G1-arrested.png step2/results/plotly/G1-arrested/pombe_G1-arrested.html running step 1... tSNE runtime: 11.708012819290161 seconds running step 2... Step 2 runtime: 6.3216712474823 seconds
------------------------ rad21-K1 Mutation ------------------
./stohic.sh data/rad21-k1_mutation/GSM1379430.matrix step1/tSNE/results/rad21-k1_mutation/pombeXYZ.txt step1/tSNE/results/rad21-k1_mutation/pombeDIST.txt step2/results/plotly/rad21-k1_mutation/pombe_rad21-K1.png step2/results/plotly/rad21-k1_mutation/pombe_rad21-K1.html running step 1... tSNE runtime: 10.761693954467773 seconds running step 2... Step 2 runtime: 6.271383047103882 seconds
------------------------ clr4 Deletion ----------------------
./stohic.sh data/clr4_deletion/GSM1379431.matrix step1/tSNE/results/clr4_deletion/pombeXYZ.txt step1/tSNE/results/clr4_deletion/pombeDIST.txt step2/results/plotly/clr4_deletion/pombe_clr4D.png step2/results/plotly/clr4_deletion/pombe_clr4D.html running step 1... tSNE runtime: 10.734359979629517 seconds running step 2... Step 2 runtime: 5.8082921504974365 seconds
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Example command line execution for MDS comparision:
------------------------ 999a WT ---------------------------
./runMDS.sh data/999a_WT/GSM1379427.matrix step1/MDS/results/999a_WT/pombeXYZ_MDS.txt step1/MDS/results/999a_WT/pombeDIST_MDS.txt step2/MDS_results/plotly/999a_WT/pombe_999aWT.png step2/MDS_results/plotly/999a_WT/pombe_999aWT.html running step 1... MDS runtime: 0.5438699722290039 seconds running step 2... Step 2 runtime: 5.708459854125977 seconds
------------------------ G1-Arrested ------------------------
./runMDS.sh data/G1-arrested/GSM1379429.matrix step1/MDS/results/G1-arrested/pombeXYZ_MDS.txt step1/MDS/results/G1-arrested/pombeDIST_MDS.txt step2/MDS_results/plotly/G1-arrested/pombe_G1-arrested.png step2/MDS_results/plotly/G1-arrested/pombe_G1-arrested.html running step 1... MDS runtime: 0.5248260498046875 seconds running step 2... Step 2 runtime: 5.871056079864502 seconds
------------------------ rad21-K1 Mutation ------------------
./runMDS.sh data/rad21-k1_mutation/GSM1379430.matrix step1/MDS/results/rad21-k1_mutation/pombeXYZ_MDS.txt step1/MDS/results/rad21-k1_mutation/pombeDIST_MDS.txt step2/MDS_results/plotly/rad21-k1_mutation/pombe_rad21-K1.png step2/MDS_results/plotly/rad21-k1_mutation/pombe_rad21-K1.html running step 1... MDS runtime: 0.5385239124298096 seconds running step 2... Step 2 runtime: 5.757267236709595 seconds
------------------------ clr4 Deletion ----------------------
./runMDS.sh data/clr4_deletion/GSM1379431.matrix step1/MDS/results/clr4_deletion/pombeXYZ_MDS.txt step1/MDS/results/clr4_deletion/pombeDIST_MDS.txt step2/MDS_results/plotly/clr4_deletion/pombe_clr4D.png step2/MDS_results/plotly/clr4_deletion/pombe_clr4D.html running step 1... MDS runtime: 0.5127038955688477 seconds running step 2... Step 2 runtime: 5.634297132492065 seconds