In [1]:
# Parameters
sample_name = "ES;ZhBTc4;untreated;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_183-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_183-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.
2019-07-23 00:37:04,385 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeZHBTC4 ES untreated
    Cell GroupES cells and embryonic tissues
    Experiment NameATAC
    Experiment GroupGEO
    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
    rep12410741734859.43175607493106870740.141467418830.0892276447520.3657
    rep22410741734859.79915358821585217710.159157535480.1074203381780.3796
    rep32410741734859.44195969881795140430.159462454790.1046223229970.374
    Modelling Metadata
    MetricValue
    auPRC0.6982
    Calibrated Recall at 50% FDR0.165
    Number of Positive Examples in Test Data177744
    Number of Negative Examples in Test Data7893107
    Imbalance Ratio in Test Data0.022
    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
Ctcf
E2f1
Tcfeb
Esrrg
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Restabsent
Trp63absent
Sox2absent
Rfx1absent
Pbx3absent
Sox9absent
Egr4absent
Zic4absent
Gabpaabsent
Klf1absent
Nfe2l2absent
Hsf1absent
Smarcc2absent
Sp3absent
Klf5absent
Rfx8absent
Unique Homer Motifs
Motif NameModiscoHomer
Foxi1absent
Zfp143absent
Pou5f1absent
Klf2absent
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_183-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_183-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_183-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 24, # seqlets: 19381, Positive for: ES;ZhBTc4;untreated;A;GEO
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_183-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_183-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_183-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 24, # seqlets: 11771, Negative for: ES;ZhBTc4;untreated;A;GEO
  • pattern_0: # seqlets: 2661 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pit1, Arid3b, Phf21a, Cux2, Dbx1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2588 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1792 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hic1, Hic2, Nfic, Nfix, Nfia

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 869 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 797 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Glis1, Zbtb7b, Zic5, Gli2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 711 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 419 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 209 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Klf1, Klf3, Klf2, Klf4, Klf8

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 207 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Ets1, Sfpi1, Erf, Bcl11a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 201 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 177 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 181 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 151 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 146 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Myc, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 143 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 100 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut1, Ahctf1, Hmg20b, Phf21a, Foxl1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 65 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 51 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 51 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 61 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Maz

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 51 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 54 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tbpl2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 49 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 37 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores