In [1]:
# Parameters
sample_name = "ENDRM_ESD;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_149-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_149-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 22:39:58,064 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeES_derived Definitive Endoderm
    Cell GroupCancer or Immortalized cells
    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
    rep11603781043278.74316366306765978430.103755243220.0868220455350.3464
    rep21603781043277.63928416936686879900.103267289560.08292545110.3476
    Modelling Metadata
    MetricValue
    auPRC0.6679
    Calibrated Recall at 50% FDR0.25
    Number of Positive Examples in Test Data104839
    Number of Negative Examples in Test Data7966012
    Imbalance Ratio in Test Data0.013
    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
Smarcc2
Sox2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Gabpaabsent
Grhl1absent
Gata2absent
Zic4absent
Sp3absent
Hsf1absent
Rfx1absent
Restabsent
Pbx3absent
Crxabsent
Mbtps2absent
Creb3absent
Foxa1absent
Pou5f1absent
Smarcc1absent
Unique Homer Motifs
Motif NameModiscoHomer
Sp2absent
E4f1absent
Erfabsent
Tbx20absent
Tcfebabsent
Tcfcp2absent
Gscabsent
Foxa2absent
Pitx2absent
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_149-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_149-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_149-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 24, # seqlets: 21568, Positive for: ENDRM_ESD;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_149-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_149-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_149-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 22, # seqlets: 7462, Negative for: ENDRM_ESD;A;GEO
  • pattern_0: # seqlets: 1953 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1307 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Maz, Zfp148, Zfp281, Sp3, Rreb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 592 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Zic5, Zic4, Zbtb7b, Glis3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 486 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 455 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox6, Sox17, Sox9, Sox3, Pbx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 386 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata2, Gata1, Gata4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 300 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 221 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Nr6a1, Nr5a1, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 226 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 205 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Nr5a1, Nr6a1, Esrrb, Esrrg

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 194 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Nr5a2, Nr6a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 192 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 155 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a1, Nr6a1, Tcfap2d, Esrrb, Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 149 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 142 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 112 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 96 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 74 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 59 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 56 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 55 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Maz

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 47 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores