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Copy file name to clipboardexpand all lines: README.md
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The repo contains the scripts to recreate the human analysis portion for the the manuscript: Regulatory activity is the default DNA state in eukaryotes. Using the raw data provided a user can create their own shuffled sequence datasets using Biasaway and then produce downstream plots. Detailed information about the set up can be found in methods section here: https://www.biorxiv.org/content/10.1101/2022.12.16.520785v1.full
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## Generating shuffled sequences
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Datasets can be found here: https://zenodo.org/records/10529931
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Datasets can be found here: https://zenodo.org/records/10535706
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To create shuffled sequence sets use `test_hg38_seqs_196kb.fasta` and biasaway (sample commands below). Test set regions (196kb each) with "N"s were filtered out to ensure proper shuffling and the surrounding flanking regions were added post shuffling.
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