In [1]:
# Parameters
sample_name = "Heart;P0;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_231-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_231-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 03:00:02,034 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeheart tissue(P0)
    Cell GroupOther Tissues
    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
    rep11899531244089.890276158991102942880.135263527670.0834290810990.3819
    rep218995312440811.45415404804496814560.179258636670.1085219829800.4069
    Modelling Metadata
    MetricValue
    auPRC0.6099
    Calibrated Recall at 50% FDR0.229
    Number of Positive Examples in Test Data141008
    Number of Negative Examples in Test Data7929843
    Imbalance Ratio in Test Data0.0175
    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
Rest
Fos
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
9430076C15Rikabsent
Pbx3absent
Irf1absent
Ets1absent
Esrrbabsent
Zfp281absent
Nficabsent
Mef2aabsent
Mbtps2absent
Bach2absent
Rfx8absent
Nfiaabsent
Pknox1absent
Rfx1absent
Gata2absent
Sp3absent
Unique Homer Motifs
Motif NameModiscoHomer
Gata6absent
Mef2dabsent
Sp2absent
Erfabsent
Creb3absent
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_231-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_231-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_231-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 23, # seqlets: 24367, Positive for: Heart;P0;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_231-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_231-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_231-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 22, # seqlets: 9339, Negative for: Heart;P0;D;En
  • pattern_0: # seqlets: 1882 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1771 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1372 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata6, Gata2, Gata4, Gata5, Gata3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1165 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 482 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

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

    Sox9, Sox17, Sox6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 299 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Nr1h2, Nr4a1, Esrrg, Nr4a3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 286 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 208 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 192 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 152 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 147 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 147 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 130 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 117 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 110 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Fos, Nfe2l2, Nfe2, Jund, Batf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 152 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 82 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 50 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 47 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 42 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 43 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hif3a

    SequenceContrib ScoresHyp_Contrib Scores