# 2026-05-22 - Claude (mhaeussl) - crPred supertrack: cis-regulatory element predictions

# This file documents all tracks under the crPred supertrack
# ("Cis-regulatory Element Predictions").
# trackDb: src/hg/makeDb/trackDb/human/hg38/crPred.ra (supertrack)
#          src/hg/makeDb/trackDb/human/hg38/tredNet.ra (TREDNet composite + subtracks)

###########################################################################
# TREDNet candidate enhancers and silencers (Huang & Ovcharenko 2024,
# PMID 38978133, https://zenodo.org/records/12523205)

    cd /hive/data/genomes/hg38/bed/crPred/tredNet

# Download
# Data from: https://zenodo.org/records/12523205
# File: SilencerEnhancer.tar.gz

    wget https://zenodo.org/records/12523205/files/SilencerEnhancer.tar.gz?download=1 \
        -O SilencerEnhancer.tar.gz
    tar xzf SilencerEnhancer.tar.gz
    mv *.bed in/

# The filenames encode ENCODE biosample ontology IDs (CL, UBERON, EFO, NTR prefixes).
# Download Cell Ontology and Uberon OBO files to resolve IDs to readable names.
# EFO and NTR IDs were resolved via the EBI OLS4 REST API and the ENCODE project API.

    wget -q http://purl.obolibrary.org/obo/cl.obo -O cl.obo
    wget -q http://purl.obolibrary.org/obo/uberon.obo -O uberon.obo

# Build the merged bigBed files (enhancer and silencer).
# The script reads all per-sample BED files, resolves IDs to names,
# merges overlapping 1-kb windows with bedtools merge, annotates each
# merged region with its contributing biosamples, and assigns colors
# by dominant sample category (tissue/cell type/cell line/mixed).

    python3 ~/kent/src/hg/makeDb/scripts/tredNet/tredNetBuild.py \
        --indir in --outdir .

# Convert to bigBed

    AS=~/kent/src/hg/makeDb/scripts/tredNet/tredNet.as
    bedToBigBed -type=bed9+4 -as=$AS -tab -extraIndex=name \
        tredNetEnhancer.bed /hive/data/genomes/hg38/chrom.sizes tredNetEnhancer.bb
    bedToBigBed -type=bed9+4 -as=$AS -tab -extraIndex=name \
        tredNetSilencer.bed /hive/data/genomes/hg38/chrom.sizes tredNetSilencer.bb

# Install

    mkdir -p /gbdb/hg38/tredNet
    ln -sf /hive/data/genomes/hg38/bed/crPred/tredNet/tredNetEnhancer.bb \
        /gbdb/hg38/tredNet/tredNetEnhancer.bb
    ln -sf /hive/data/genomes/hg38/bed/crPred/tredNet/tredNetSilencer.bb \
        /gbdb/hg38/tredNet/tredNetSilencer.bb
