In [1]:
# Parameters
sample_name = "CH12.LX;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_271-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_271-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 04:59:22,151 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeCH12.LX cell line
    Cell GroupCancer or Immortalized cells
    Experiment NameDHS
    Experiment GroupENCODE
    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
    rep115150410464722.88641028972231969200.31119571470.190446772110.4551
    rep1015150410464720.9964625700215780720.252610616660.1727787230.4448
    rep1115150410464720.011538784112218700.22728867760.164923849200.4434
    rep215150410464723.172979330431226900.319218603630.190244348860.4534
    rep315150410464722.49851037521931662640.305519499080.188246974460.4533
    rep415150410464727.2006366292910750330.2947475960.204516621930.4546
    rep515150410464723.7453960281131112550.324418830800.196343881370.4575
    rep615150410464723.08111000124832215090.322519063070.190845508650.4555
    rep715150410464724.3368860370627638680.321617328570.201639404510.4585
    rep815150410464722.52351018801432509320.319519231840.18946222980.4542
    rep915150410464719.76876029124052930.274914368800.164238853760.4441
    Modelling Metadata
    MetricValue
    auPRC0.5747
    Calibrated Recall at 50% FDR0.232
    Number of Positive Examples in Test Data128267
    Number of Negative Examples in Test Data7942584
    Imbalance Ratio in Test Data0.0159
    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
Mbtps2
Creb3
Ctcf
Smarcc2
Ebf1
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Hsf1absent
Restabsent
Bcl11aabsent
Trp73absent
Smarcc1absent
Sp3absent
Relbabsent
Mef2dabsent
Erfabsent
Tbpl2absent
Tcfebabsent
Sfpi1absent
Rfx1absent
Unique Homer Motifs
Motif NameModiscoHomer
Elk1absent
E2f5absent
Klf5absent
Fosabsent
Hivep1absent
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_271-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_271-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_271-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 22, # seqlets: 29945, Positive for: CH12.LX;D;En
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_271-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_271-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_271-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 18, # seqlets: 8786, Negative for: CH12.LX;D;En
  • pattern_0: # seqlets: 1753 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Zbtb7b, Glis1, Zbtb7a, Gli2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1487 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1336 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Scrt1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1121 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Dbx1, Tlx2, Sebox, Arid3b, Lhx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 927 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tbpl2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 463 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Atoh1, Ferd3l, Tcfap4, Nhlh2, Ascl2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 339 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 338 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Batf, Nfe2, Fos, Jund

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 240 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxm1, Foxj1, Foxp4, Onecut2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 145 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp410

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 165 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 121 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 131 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 52 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 50 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1, Runx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 30 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores