fasta_file: ../data/mm10_no_alt_analysis_set_ENCODE.fasta

task_specs:

  Oct4:

    tracks:

      - ../data/chip-seq/Oct4/counts.pos.bw

      - ../data/chip-seq/Oct4/counts.neg.bw

    peaks: ../data/chip-seq/Oct4/idr-optimal-set.summit.bed.gz

  Sox2:

    tracks:

      - ../data/chip-seq/Sox2/counts.pos.bw

      - ../data/chip-seq/Sox2/counts.neg.bw

    peaks: ../data/chip-seq/Sox2/idr-optimal-set.summit.bed.gz

  Nanog:

    tracks:

      - ../data/chip-seq/Nanog/counts.pos.bw

      - ../data/chip-seq/Nanog/counts.neg.bw

    peaks: ../data/chip-seq/Nanog/idr-optimal-set.summit.bed.gz

bias_specs:

  input:

    tracks:

      - ../data/chip-seq/input-control/counts.pos.bw

      - ../data/chip-seq/input-control/counts.neg.bw

    tasks:

      - Oct4

      - Sox2

      - Nanog