In [1]:
# Parameters
sample_name = "G_NRN_P;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_178-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_178-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 00:18:21,052 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeGranule Neuron Progenitors (wt)
    Cell GroupNeural Cells and 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
    rep119147212931416.71663176226374606740.23544392960.1399131292680.4136
    rep219147212931417.01272478209950279980.20334690910.140198999100.3998
    rep319147212931410.94654035375848988540.121537743360.0936149813790.3714
    Modelling Metadata
    MetricValue
    auPRC0.6524
    Calibrated Recall at 50% FDR0.203
    Number of Positive Examples in Test Data152841
    Number of Negative Examples in Test Data7918010
    Imbalance Ratio in Test Data0.0189
    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
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Erfabsent
Sox3absent
Pbx3absent
Sp3absent
Klf16absent
Tcfebabsent
Smarcc2absent
Mbtps2absent
Rfx1absent
Nfibabsent
Esx1absent
Neurod1absent
Zic1absent
E2f1absent
Creb3absent
Tbpl2absent
Unique Homer Motifs
Motif NameModiscoHomer
Hes7absent
E4f1absent
Mbd2absent
Sp2absent
Zfp143absent
Nficabsent
Mbd1absent
Ferd3labsent
Gabpaabsent
Vsx2absent
Bhlhe22absent
Rfx2absent
Klf13absent
Zfxabsent
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_178-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_178-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_178-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 21, # seqlets: 16766, Positive for: G_NRN_P;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_178-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_178-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_178-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 28, # seqlets: 13173, Negative for: G_NRN_P;A;GEO
  • pattern_0: # seqlets: 2144 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1850 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1263 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rarb, Nr2f2, Rara, Nr2f1, Nr2f6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1253 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp238, Tcf21, Tcf4, Bhlha15, Twist2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 1001 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 923 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 662 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 650 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b, Arid3b, Tbp, Onecut1, Pit1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 526 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 469 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1, Nr5a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 444 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 331 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 285 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfic

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 278 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 238 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 117 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Ets1, Erf, Sfpi1, Bcl11a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 111 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 91 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 83 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 69 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 63 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 60 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 66 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Egr2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata2, Gata6, Gata1, Gata5, Gata4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_24: # seqlets: 35 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_25: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Spib

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_26: # seqlets: 40 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxi1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_27: # seqlets: 31 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores