imadsconf.yaml

binding_max_offset: 5000
download_dir: /tmp/pred_data
genome_data:
- alias_url: ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/non_alt_loci_set.txt
  ftp_files:
  - goldenPath/hg19/database/knownGene.txt.gz
  - goldenPath/hg19/database/kgXref.txt.gz
  gene_lists:
  - common_lookup_table: kgxref
    common_lookup_table_field: kgid
    common_name: genesymbol
    name: UCSC Known Genes
    source_table: knowngene
  genome: hg19
  genome_file: goldenPath/hg19/bigZips/hg19.2bit
  prediction_lists:
  - core_length: 6
    core_offset: 7
    family: bHLH
    fix_script: bigBedToBed
    name: c-Myc_0001
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.6
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg19/hg19_0001_c-Myc.bb
  - core_length: 6
    core_offset: 7
    family: bHLH
    fix_script: bigBedToBed
    name: Mad1_0002
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.6
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg19/hg19_0002_Mad1.bb
  - core_length: 6
    core_offset: 7
    family: bHLH
    fix_script: bigBedToBed
    name: Max_0003
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.6
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg19/hg19_0003_Max.bb
  - core_length: 6
    core_offset: 7
    family: bHLH
    fix_script: bigBedToBed
    name: Mad1_0002_vs_c-Myc_0001
    preference_max: 6.85
    preference_min: -12.14
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg19/hg19_Mad1_0002_vs_c-Myc_0001.bb
  - core_length: 6
    core_offset: 7
    family: bHLH
    fix_script: bigBedToBed
    name: Mad1_0002_vs_Max_0003
    preference_max: 6.28
    preference_min: -7.43
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg19/hg19_Mad1_0002_vs_Max_0003.bb
  - core_length: 6
    core_offset: 7
    family: bHLH
    fix_script: bigBedToBed
    name: Max_0003_vs_c-Myc_0001
    preference_max: 8.59
    preference_min: -8.24
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg19/hg19_Max_0003_vs_c-Myc_0001.bb
  - core_length: 4
    core_offset: 8
    family: ETS
    fix_script: bigBedToBed
    name: Elk1_0004
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.8
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg19/hg19_0004_Elk1.bb
  - core_length: 4
    core_offset: 8
    family: ETS
    fix_script: bigBedToBed
    name: Ets1_0005
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.8
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg19/hg19_0005_Ets1.bb
  - core_length: 4
    core_offset: 8
    family: ETS
    fix_script: bigBedToBed
    name: Gabpa_0006
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.6
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg19/hg19_0006_Gabpa.bb
  - core_length: 4
    core_offset: 8
    family: ETS
    fix_script: bigBedToBed
    name: Elk1_0004_vs_Ets1_0005
    preference_max: 25.3
    preference_min: -17.24
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg19/hg19_Elk1_0004_vs_Ets1_0005.bb
  - core_length: 4
    core_offset: 8
    family: ETS
    fix_script: bigBedToBed
    name: Elk1_0004_vs_Gabpa_0006
    preference_max: 15.66
    preference_min: -13.29
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg19/hg19_Elk1_0004_vs_Gabpa_0006.bb
  - core_length: 4
    core_offset: 8
    family: ETS
    fix_script: bigBedToBed
    name: Ets1_0005_vs_Gabpa_0006
    preference_max: 15.85
    preference_min: -19.33
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg19/hg19_Ets1_0005_vs_Gabpa_0006.bb
  - core_length: 4
    core_offset: 8
    family: E2F
    fix_script: bigBedToBed
    name: E2f1_0007
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.6
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg19/hg19_0007_E2f1.bb
  - core_length: 4
    core_offset: 8
    family: E2F
    fix_script: bigBedToBed
    name: E2f3_0008
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.75
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg19/hg19_0008_E2f3.bb
  - core_length: 4
    core_offset: 8
    family: E2F
    fix_script: bigBedToBed
    name: E2f4_0009
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.65
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg19/hg19_0009_E2f4.bb
  - core_length: 4
    core_offset: 8
    family: E2F
    fix_script: bigBedToBed
    name: E2f1_0007_vs_E2f4_0009
    preference_max: 9.88
    preference_min: -11.44
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg19/hg19_E2f1_0007_vs_E2f4_0009.bb
  - core_length: 4
    core_offset: 8
    family: E2F
    fix_script: bigBedToBed
    name: E2f1_0007_vs_E2f3_0008
    preference_max: 9.59
    preference_min: -16.98
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg19/hg19_E2f1_0007_vs_E2f3_0008.bb
  - core_length: 4
    core_offset: 8
    family: E2F
    fix_script: bigBedToBed
    name: E2f3_0008_vs_E2f4_0009
    preference_max: 8.33
    preference_min: -8.05
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg19/hg19_E2f3_0008_vs_E2f4_0009.bb
  - core_length: 5
    core_offset: 8
    family: RUNX
    fix_script: bigBedToBed
    name: Runx1_0010
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.7
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg19/hg19_0010_Runx1.bb
  - core_length: 5
    core_offset: 8
    family: RUNX
    fix_script: bigBedToBed
    name: Runx2_0011
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.8
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg19/hg19_0011_Runx2.bb
  - core_length: 5
    core_offset: 8
    family: RUNX
    fix_script: bigBedToBed
    name: Runx1_0010_vs_Runx2_0011
    preference_max: 4.36
    preference_min: -3.6
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg19/hg19_Runx1_0010_vs_Runx2_0011.bb
  trackhub_url:
  - predictions: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hub.txt
  - preferences: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences/hub.txt
- alias_url: ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/non_alt_loci_set.txt
  ftp_files:
  - goldenPath/hg38/database/wgEncodeGencodeBasicV23.txt.gz
  - goldenPath/hg38/database/wgEncodeGencodeCompV23.txt.gz
  - goldenPath/hg38/database/knownGene.txt.gz
  - goldenPath/hg38/database/kgXref.txt.gz
  - goldenPath/hg38/database/refGene.txt.gz
  gene_lists:
  - common_lookup_table: kgxref
    common_lookup_table_field: kgid
    common_name: genesymbol
    name: UCSC Known Genes
    source_table: knowngene
  - common_name: name2
    name: Reference Genes
    source_table: refgene
  - common_name: name2
    name: Gencode V23 Basic Genes
    source_table: wgEncodeGencodeBasicV23
  - common_name: name2
    name: Gencode V23 Comprehensive Genes
    source_table: wgEncodeGencodeCompV23
  genome: hg38
  genome_file: goldenPath/hg38/bigZips/hg38.2bit
  prediction_lists:
  - core_length: 6
    core_offset: 7
    family: bHLH
    fix_script: bigBedToBed
    name: c-Myc_0001
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.6
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg38/hg38_0001_c-Myc.bb
  - core_length: 6
    core_offset: 7
    family: bHLH
    fix_script: bigBedToBed
    name: Mad1_0002
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.6
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg38/hg38_0002_Mad1.bb
  - core_length: 6
    core_offset: 7
    family: bHLH
    fix_script: bigBedToBed
    name: Max_0003
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.6
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg38/hg38_0003_Max.bb
  - core_length: 6
    core_offset: 7
    family: bHLH
    fix_script: bigBedToBed
    name: Mad1_0002_vs_c-Myc_0001
    preference_max: 6.85
    preference_min: -12.14
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg38/hg38_Mad1_0002_vs_c-Myc_0001.bb
  - core_length: 6
    core_offset: 7
    family: bHLH
    fix_script: bigBedToBed
    name: Mad1_0002_vs_Max_0003
    preference_max: 6.28
    preference_min: -7.43
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg38/hg38_Mad1_0002_vs_Max_0003.bb
  - core_length: 6
    core_offset: 7
    family: bHLH
    fix_script: bigBedToBed
    name: Max_0003_vs_c-Myc_0001
    preference_max: 8.59
    preference_min: -8.24
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg38/hg38_Max_0003_vs_c-Myc_0001.bb
  - core_length: 4
    core_offset: 8
    family: ETS
    fix_script: bigBedToBed
    name: Elk1_0004
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.8
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg38/hg38_0004_Elk1.bb
  - core_length: 4
    core_offset: 8
    family: ETS
    fix_script: bigBedToBed
    name: Ets1_0005
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.8
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg38/hg38_0005_Ets1.bb
  - core_length: 4
    core_offset: 8
    family: ETS
    fix_script: bigBedToBed
    name: Gabpa_0006
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.6
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg38/hg38_0006_Gabpa.bb
  - core_length: 4
    core_offset: 8
    family: ETS
    fix_script: bigBedToBed
    name: Elk1_0004_vs_Ets1_0005
    preference_max: 25.3
    preference_min: -17.24
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg38/hg38_Elk1_0004_vs_Ets1_0005.bb
  - core_length: 4
    core_offset: 8
    family: ETS
    fix_script: bigBedToBed
    name: Elk1_0004_vs_Gabpa_0006
    preference_max: 15.66
    preference_min: -13.29
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg38/hg38_Elk1_0004_vs_Gabpa_0006.bb
  - core_length: 4
    core_offset: 8
    family: ETS
    fix_script: bigBedToBed
    name: Ets1_0005_vs_Gabpa_0006
    preference_max: 15.85
    preference_min: -19.33
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg38/hg38_Ets1_0005_vs_Gabpa_0006.bb
  - core_length: 4
    core_offset: 8
    family: E2F
    fix_script: bigBedToBed
    name: E2f1_0007
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.6
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg38/hg38_0007_E2f1.bb
  - core_length: 4
    core_offset: 8
    family: E2F
    fix_script: bigBedToBed
    name: E2f3_0008
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.75
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg38/hg38_0008_E2f3.bb
  - core_length: 4
    core_offset: 8
    family: E2F
    fix_script: bigBedToBed
    name: E2f4_0009
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.65
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg38/hg38_0009_E2f4.bb
  - core_length: 4
    core_offset: 8
    family: E2F
    fix_script: bigBedToBed
    name: E2f1_0007_vs_E2f4_0009
    preference_max: 9.88
    preference_min: -11.44
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg38/hg38_E2f1_0007_vs_E2f4_0009.bb
  - core_length: 4
    core_offset: 8
    family: E2F
    fix_script: bigBedToBed
    name: E2f1_0007_vs_E2f3_0008
    preference_max: 9.59
    preference_min: -16.98
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg38/hg38_E2f1_0007_vs_E2f3_0008.bb
  - core_length: 4
    core_offset: 8
    family: E2F
    fix_script: bigBedToBed
    name: E2f3_0008_vs_E2f4_0009
    preference_max: 8.33
    preference_min: -8.05
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg38/hg38_E2f3_0008_vs_E2f4_0009.bb
  - core_length: 5
    core_offset: 8
    family: RUNX
    fix_script: bigBedToBed
    name: Runx1_0010
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.7
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg38/hg38_0010_Runx1.bb
  - core_length: 5
    core_offset: 8
    family: RUNX
    fix_script: bigBedToBed
    name: Runx2_0011
    preference_max: ''
    preference_min: ''
    sort_max_guess: 0.8
    type: PREDICTION
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hg38/hg38_0011_Runx2.bb
  - core_length: 5
    core_offset: 8
    family: RUNX
    fix_script: bigBedToBed
    name: Runx1_0010_vs_Runx2_0011
    preference_max: 4.36
    preference_min: -3.6
    sort_max_guess: 16
    type: PREFERENCE
    url: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences//hg38/hg38_Runx1_0010_vs_Runx2_0011.bb
  trackhub_url:
  - predictions: http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hub.txt
  - preferences: http://trackhub.genome.duke.edu/gordanlab/tf-dna-preferences/hub.txt
model_base_url: https://zenodo.org/record/3405516/files
model_tracks_url_list:
- https://zenodo.org/record/3405516/files/tracks-predictions.yaml
- https://zenodo.org/record/3405516/files/tracks-preferences.yaml