fasta_file: /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa
task_specs:
  task1:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/GM12878-MAX-human-ENCSR000DZF-Rep1.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/GM12878-MAX-human-ENCSR000DZF-Rep1.unique.abs_minus.bigWig
    peaks: hg19-peak-files/GM12878-MAX-human-ENCSR000DZF-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task2:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/GM12878-MAX-human-ENCSR000DZF-Rep2.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/GM12878-MAX-human-ENCSR000DZF-Rep2.unique.abs_minus.bigWig
    peaks: hg19-peak-files/GM12878-MAX-human-ENCSR000DZF-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task3:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/H1-hESC-MAX-human-ENCSR000EUP-Rep1.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/H1-hESC-MAX-human-ENCSR000EUP-Rep1.unique.abs_minus.bigWig
    peaks: hg19-peak-files/H1-hESC-MAX-human-ENCSR000EUP-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task4:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/H1-hESC-MAX-human-ENCSR000EUP-Rep2.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/H1-hESC-MAX-human-ENCSR000EUP-Rep2.unique.abs_minus.bigWig
    peaks: hg19-peak-files/H1-hESC-MAX-human-ENCSR000EUP-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task5:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/HeLa-S3-MAX-human-ENCSR000ECN-Rep1.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/HeLa-S3-MAX-human-ENCSR000ECN-Rep1.unique.abs_minus.bigWig
    peaks: hg19-peak-files/HeLa-S3-MAX-human-ENCSR000ECN-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task6:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/HeLa-S3-MAX-human-ENCSR000ECN-Rep2.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/HeLa-S3-MAX-human-ENCSR000ECN-Rep2.unique.abs_minus.bigWig
    peaks: hg19-peak-files/HeLa-S3-MAX-human-ENCSR000ECN-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task7:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/HepG2-MAX-human-ENCSR000EDS-Rep1.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/HepG2-MAX-human-ENCSR000EDS-Rep1.unique.abs_minus.bigWig
    peaks: hg19-peak-files/HepG2-MAX-human-ENCSR000EDS-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task8:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/HepG2-MAX-human-ENCSR000EDS-Rep2.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/HepG2-MAX-human-ENCSR000EDS-Rep2.unique.abs_minus.bigWig
    peaks: hg19-peak-files/HepG2-MAX-human-ENCSR000EDS-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task9:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/K562-MAX-human-ENCSR000BLP-Rep1.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/K562-MAX-human-ENCSR000BLP-Rep1.unique.abs_minus.bigWig
    peaks: hg19-peak-files/K562-MAX-human-ENCSR000BLP-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task10:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/K562-MAX-human-ENCSR000BLP-Rep2.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/K562-MAX-human-ENCSR000BLP-Rep2.unique.abs_minus.bigWig
    peaks: hg19-peak-files/K562-MAX-human-ENCSR000BLP-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task11:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/K562-MAX-human-ENCSR000EFV-Rep1.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/K562-MAX-human-ENCSR000EFV-Rep1.unique.abs_minus.bigWig
    peaks: hg19-peak-files/K562-MAX-human-ENCSR000EFV-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task12:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/K562-MAX-human-ENCSR000EFV-Rep2.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/K562-MAX-human-ENCSR000EFV-Rep2.unique.abs_minus.bigWig
    peaks: hg19-peak-files/K562-MAX-human-ENCSR000EFV-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task13:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/NB4-MAX-human-ENCSR000EHS-Rep1.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/NB4-MAX-human-ENCSR000EHS-Rep1.unique.abs_minus.bigWig
    peaks: hg19-peak-files/NB4-MAX-human-ENCSR000EHS-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task14:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/NB4-MAX-human-ENCSR000EHS-Rep2.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/NB4-MAX-human-ENCSR000EHS-Rep2.unique.abs_minus.bigWig
    peaks: hg19-peak-files/NB4-MAX-human-ENCSR000EHS-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task15:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/endothelial_cell_of_umbilical_vein-MAX-human-ENCSR000EEZ-Rep1.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/endothelial_cell_of_umbilical_vein-MAX-human-ENCSR000EEZ-Rep1.unique.abs_minus.bigWig
    peaks: hg19-peak-files/endothelial_cell_of_umbilical_vein-MAX-human-ENCSR000EEZ-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task16:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/endothelial_cell_of_umbilical_vein-MAX-human-ENCSR000EEZ-Rep2.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/endothelial_cell_of_umbilical_vein-MAX-human-ENCSR000EEZ-Rep2.unique.abs_minus.bigWig
    peaks: hg19-peak-files/endothelial_cell_of_umbilical_vein-MAX-human-ENCSR000EEZ-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task17:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/liver-MAX-human-ENCSR521IID-Rep1.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/liver-MAX-human-ENCSR521IID-Rep1.unique.abs_minus.bigWig
    peaks: hg19-peak-files/liver-MAX-human-ENCSR521IID-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task18:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/liver-MAX-human-ENCSR521IID-Rep2.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/liver-MAX-human-ENCSR521IID-Rep2.unique.abs_minus.bigWig
    peaks: hg19-peak-files/liver-MAX-human-ENCSR521IID-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task19:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/liver-MAX-human-ENCSR847DIT-Rep1.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/liver-MAX-human-ENCSR847DIT-Rep1.unique.abs_minus.bigWig
    peaks: hg19-peak-files/liver-MAX-human-ENCSR847DIT-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
  task20:
    pos_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/liver-MAX-human-ENCSR847DIT-Rep2.unique.plus.bigWig
    neg_counts: /oak/stanford/groups/akundaje/marinovg/TF-models/2018-11-05-ENCODE-TF-ChIP-seq-for-BPNet/liver-MAX-human-ENCSR847DIT-Rep2.unique.abs_minus.bigWig
    peaks: hg19-peak-files/liver-MAX-human-ENCSR847DIT-optimal_idr.bed
    # optional
    ignore_strand: False
    bias_bigwig:
    bias_model: null
