encode

ENCODE feature generation and preprocessing

Here are instructions to reproduce the Codalab bundle, in a directory path BUNDLE_ROOT_DIRECTORY.

Download the human genome sequence (hg19 assembly) in FASTA format from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigZips/hg19.fa.gz and extract it into SEQUENCE_PATH.
Run python prep_sequence.py --seq_path SEQUENCE_PATH --output_dir OUTPUT_DIR to write the fasta file found in SEQUENCE_PATH to a numpy array archive in OUTPUT_PATH. (The dataset loader assumes OUTPUT_PATH to be <bundle root directory>/sequence.npz.)
Download the DNase accessibility data. This consists of whole-genome DNase files in bigwig format from https://guanfiles.dcmb.med.umich.edu/Leopard/dnase_bigwig/. Save these to filenames <bundle root directory>/DNASE.<celltype>.fc.signal.bigwig in the code.
Run python prep_accessibility.py. This writes samples of each bigwig file to <bundle root directory>/qn.<celltype>.npy. These are used at runtime when the dataset loader is initialized, to perform quantile normalization on the DNase accessibility signals.
Download the labels from the challenge into a label directory <bundle root directory>/labels/ created for this purpose:

The training chromosome labels for the challenge's training cell types from https://www.synapse.org/#!Synapse:syn7413983 for the relevant transcription factor ( https://www.synapse.org/#!Synapse:syn7415202 for the TF MAX, downloaded as MAX.train.labels.tsv.gz ).
The training chromosome labels for the challenge's evaluation cell type (liver) from https://www.synapse.org/#!Synapse:syn8077511 for the relevant transcription factor ( https://www.synapse.org/#!Synapse:syn8077648 for the TF MAX, downloaded as MAX.train_wc.labels.tsv.gz ).
The validation chromosome labels for the challenge's training cell types from https://www.synapse.org/#!Synapse:syn8441154 for the relevant transcription factor ( https://www.synapse.org/#!Synapse:syn8442103 for the TF MAX, downloaded as MAX.val.labels.tsv.gz ).
The validation chromosome labels for the challenge's evaluation cell type (liver) from https://www.synapse.org/#!Synapse:syn8442975 for the relevant transcription factor ( https://www.synapse.org/#!Synapse:syn8443021 for the TF MAX, downloaded as MAX.test.labels.tsv.gz ).