In [1]:
# Parameters
sample_name = "Adrenal;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_59-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_59-naivegw/NaiveauPRC.txt"
homer_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_scans"
In [2]:
from matlas.modisco_report import modisco_report_pipeline, display_metadata
reportfile= "/mnt/lab_data/kundaje/msharmin/mouse_hem/with_tfd/full_mouse50/filtering samples_MS2.xlsx"
sheetname = "filter23"

load data from labcluster

Using TensorFlow backend.
2019-07-22 18:06:01,530 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeAdrenal
    Cell GroupOther Tissues
    Experiment NameATAC
    Experiment GroupCasellas Lab
    Pipeline Output
    replicateNaïve overlap peaksIDR peaksTSS enrichment (< 8 is very poor <10 is low)Final number of unique mapping, dup-filtered, chrM filtered readsNumber of reads in called peak regionsFraction of reads in called peak regionsNumber of reads in promoter regionsFraction of reads in promoter regionsNumber of reads in enhancer regionsFraction of reads in enhancer regions
    rep117940212108113.775356511037118559860.209964306530.1138219678600.3889
    Modelling Metadata
    MetricValue
    auPRC0.6136
    Calibrated Recall at 50% FDR0.208
    Number of Positive Examples in Test Data140042
    Number of Negative Examples in Test Data7930809
    Imbalance Ratio in Test Data0.0174
    Test Chromosomeschr2, chr3, chr19
In [4]:
from matlas.modisco_report import display_comparative_motif_sets
display_comparative_motif_sets(sample_name, homer_root, modisco_root)

TF-MoDISco is using the TensorFlow backend.
Number of CISBP motifs obtained by TF-MoDISco and Homer-denovo
Shared Motifs
Motif NameModiscoHomer
Pbx3
Ctcf
Sp3
Fos
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Irf1absent
Mbtps2absent
Nfiaabsent
Nfat5absent
Hoxc9absent
Rfx1absent
Creb3absent
Mef2dabsent
Cebpbabsent
Smarcc2absent
Nr5a1absent
Ets1absent
Unique Homer Motifs
Motif NameModiscoHomer
Cebpgabsent
E4f1absent
Zfp161absent
Zfp143absent
Esrrbabsent
Gabpaabsent
In [5]:
modisco_report_pipeline(sample_name, modisco_root, mitra_subdir, task_dir, database_name, 
                        importance=True, render=True)

rsync -t -av /srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019/task_59-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_59-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_59-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 18, # seqlets: 19076, Positive for: Adrenal;A;CL
In [6]:
modisco_report_pipeline(sample_name, modisco_root, mitra_subdir, task_dir, database_name, 
                        importance=False, render=True)

rsync -t -av /srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019/task_59-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_59-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_59-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 25, # seqlets: 12617, Negative for: Adrenal;A;CL
  • pattern_0: # seqlets: 1740 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Zbtb7a, Zbtb7b, Glis1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1702 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1504 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Yy1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 940 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637, Hmg20b, Tbp

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 901 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Nr1h2, Nr2f6, Rarb, Esrrg

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 869 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a1, Nr5a2, Esrrb, Nr6a1, Esrrg

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 778 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7c, Gli3, Gli1, Gli2, Hic2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 441 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 422 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2, Nfe2l2, Jund, Fosl1, Fos

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 389 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pbx3, Foxi1, Dux, Ybx1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 381 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut1, Onecut3, Onecut2, Cux2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 362 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 299 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Nr6a1, Esrrb, Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 292 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 263 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b, Onecut1, Onecut3, Ahctf1, Foxc2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 245 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637, Tbp, Hmg20b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 207 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 178 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 150 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637, Hmg20b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 145 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 123 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 77 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Klf1, Klf4, Klf3, Klf2, Klf12

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 76 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 87 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_24: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Ets1, Fev, Sfpi1, Erf

    SequenceContrib ScoresHyp_Contrib Scores