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imadsconf.yaml
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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