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README.txt | ||
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blueprint.decode | ||
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encode.decode | ||
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erc.decode | ||
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erc2-H3-all.decode | ||
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erc2-H3K27me3.decode | ||
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erc2-H3K36me3.decode | ||
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erc2-H3K4me1.decode | ||
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erc2-H3K4me3.decode | ||
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erc2-H3K9me3.decode | ||
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erc2.decode | ||
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init_db.pl | ||
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load_450k_array.pl | ||
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load_dataset.pl | ||
README.txt
This directory contains the scripts and files necessary to rebuild the eFORGE database from scratch. In summary, the steps are: - Create an empty DB - Load the information about the arrays - Load the dataset with DHS, Histone peaks, etc - Move the DB to its final destination 1. CREATE AN EMPTY DATABASE Please refer to the help of init_db.pl for information about the different options rm eforge_1.1.db perl init_db.pl --db_name eforge_1.1.db 2. LOAD THE ARRAYS Please refer to the help of load_450k_array.pl for information about the different options perl load_450k_array.pl --work_dir input 3. LOAD THE DATASETS Please refer to the help of load_dataset.pl for information about the different options perl load_dataset.pl --db_name eforge_1.1.db --tag erc --name 'Roadmap Epigenomics (2012 data) - DHS' --decode_file erc.decode --work_dir input/erc/ perl load_dataset.pl --db_name eforge_1.1.db --tag encode --name 'ENCODE - DHS' --decode_file encode.decode --work_dir input/encode/ perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-DHS --name 'Consolidated Roadmap Epigenomics - DHS' --decode_file erc2.decode --work_dir input/erc2/ perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3K27me3 --name 'Consolidated Roadmap Epigenomics - H3K27me3' --decode_file erc2-H3K27me3.decode --work_dir input/erc2/ perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3K36me3 --name 'Consolidated Roadmap Epigenomics - H3K36me3' --decode_file erc2-H3K36me3.decode --work_dir input/erc2/ perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3K4me3 --name 'Consolidated Roadmap Epigenomics - H3K4me3' --decode_file erc2-H3K4me3.decode --work_dir input/erc2/ perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3K9me3 --name 'Consolidated Roadmap Epigenomics - H3K9me3' --decode_file erc2-H3K9me3.decode --work_dir input/erc2/ perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3K4me1 --name 'Consolidated Roadmap Epigenomics - H3K4me1' --decode_file erc2-H3K4me1.decode --work_dir input/erc2/ perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3-all --name 'Consolidated Roadmap Epigenomics - All H3 marks' --decode_file erc2-H3-all.decode --work_dir input/erc2/ 4. MOVE THE DATABASE TO ITS FINAL LOCATION mv eforge_1.1.db ..