In [1]:
# Parameters
sample_name = "CH12;med14;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_92-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_92-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 19:50:27,715 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typech12 med14 mt
    Cell GroupCancer or Immortalized cells
    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
    rep1110526851596.3964195773338NANANANANANA
    Modelling Metadata
    MetricValue
    auPRC0.6213
    Calibrated Recall at 50% FDR0.217
    Number of Positive Examples in Test Data39445
    Number of Negative Examples in Test Data8031406
    Imbalance Ratio in Test Data0.0049
    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
Tbpl2
Ctcf
Pbx3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Mbtps2absent
Relbabsent
Tcfecabsent
Zfp281absent
Mef2aabsent
Sp2absent
Sfpi1absent
Ebf1absent
Irf1absent
Fosabsent
Rfx1absent
Smarcc2absent
Creb3absent
Unique Homer Motifs
Motif NameModiscoHomer
Elk1absent
Sim1absent
Hivep1absent
Klf5absent
Zfp143absent
Yy1absent
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_92-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_92-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_92-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 18, # seqlets: 24315, Positive for: CH12;med14;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_92-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_92-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_92-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 19, # seqlets: 5257, Negative for: CH12;med14;A;CL
  • pattern_0: # seqlets: 1874 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 725 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 583 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Zbtb7b, Glis1, Zbtb7a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 358 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tbp, Ahctf1, Hmg20b, Dmrt2, Pit1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 336 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b, Tbp, Arid3b, Dbx1, Ahctf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 228 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b, Tbp, Phf21a, Dbx1, Ahctf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 197 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 200 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b, Dbx1, Tlx2, Onecut1, Hmg20b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 125 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 117 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 95 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 78 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zscan4, Egr2, Zscan4c

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 68 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 65 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 47 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 40 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcfap2a, Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 37 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 50 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 34 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores