In [1]:
# Parameters
sample_name = "FBRBLST;8wks;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_220-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_220-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 02:25:14,567 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeFibroblast (adult-8wks)
    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
    rep116714810923014.97122390696277423660.324132292530.1352120671230.5052
    rep216714810923011.95162045087756452870.276319160600.093897976340.4795
    Modelling Metadata
    MetricValue
    auPRC0.5443
    Calibrated Recall at 50% FDR0.258
    Number of Positive Examples in Test Data154561
    Number of Negative Examples in Test Data7916290
    Imbalance Ratio in Test Data0.0192
    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
Smarcc2
Fos
Ctcf
Sp3
Runx2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Ets1absent
Mef2cabsent
Mbtps2absent
Bach2absent
Nfiaabsent
Relabsent
Cebpbabsent
Creb3absent
Rfx1absent
Hsf1absent
Irf1absent
Bhlha15absent
Nfatc2absent
Nficabsent
Sox3absent
Unique Homer Motifs
Motif NameModiscoHomer
Yy1absent
Cebpgabsent
Creb1absent
Mef2babsent
Zfp523absent
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_220-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_220-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_220-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 25, # seqlets: 21701, Positive for: FBRBLST;8wks;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_220-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_220-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_220-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 26, # seqlets: 10581, Negative for: FBRBLST;8wks;D;En
  • pattern_0: # seqlets: 1822 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Scrt1, Scrt2, Id4, Atoh8, Mesp2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1458 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Dbx1, Pou4f1, Arid3b, Tlx2, Sebox

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1248 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 993 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata4, Gata1, Gata5, Gata3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 942 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox9, Sox17

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 839 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 749 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 682 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 435 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Nfe2, Jund, Batf, Fos

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 279 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 151 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 95 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 89 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfic

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 85 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1, Runx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 76 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Egr2, Hif3a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 76 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 74 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 65 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 62 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 65 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 74 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 50 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 41 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_24: # seqlets: 51 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Wt1, Sp3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_25: # seqlets: 36 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Egr2

    SequenceContrib ScoresHyp_Contrib Scores