Functional Identification of Non-coding Sequences Using Random Forests

This page contains the set of data required to run FINSURF on your own variants using finsurf.py, and plot feature contributions for each individual variant using plot_contribution.py.

Data for finsurf.py

After cloning the FINSURF gitHub repository, download the following files to analyze your personnal variants in bed format:


            
            
             finsurf_dataV1.tgz (4.8 Gb)  
            
            
             CHECKSUMS

Once downloaded, go to the finsurf directory and extract the files:


            
            tar -xzvf finsurf_dataV1.tgz

should extract this data set:


            
            static/data/scores_all_chroms_1e-4.tsv.gz
            static/data/scores_all_chroms_1e-4.tsv.gz.tbi
            static/data/FINSURF_REGULATORY_REGIONS_GENES.bed.gz
            static/data/FINSURF_REGULATORY_REGIONS_GENES.bed.gz.tbi

Data for plot_contribution.py

The plot_contribution.py python script will need very large files of data. A tar archive is available here:


            
            
             plot_contribution_dataV1.tgz (84 Go)  
            
            
             CHECKSUMS  
            
            
            Once downloaded, go to the finsurf directory and extract the files:
            

            
            

            
            tar -xzvf plot_contribution_dataV1.tgz
            
            

            

            should extract this data set:
            

            
            
            static/data/FINSURF_model_objects/full-model_woTargs_columns.txt
            static/data/FINSURF_model_objects/rename_columns_model.tsv
            static/data/FULL_FC_transition.tsv.gz
            static/data/FULL_FC_transition.tsv.gz.tbi
            static/data/FULL_FC_transversion.tsv.gz
            static/data/FULL_FC_transversion.tsv.gz.tbi
            static/data/NUM_FEATURES.tsv.gz
            static/data/NUM_FEATURES.tsv.gz.tbi
            static/data/SCALED_NUM_FEATURES.tsv.gz
            static/data/SCALED_NUM_FEATURES.tsv.gz.tbi
            

            
            
            
	
		Click here to contact us