In [1]:
# Parameters
sample_name = "LRG_INTSTN;8wks;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_263-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_263-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 04:33:37,898 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeLarge Intestine (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
    rep11285558943613.74142845286559434000.20930686180.1079115613820.4066
    rep2128555894368.13633430670648336680.14135152610.1025134709840.3929
    Modelling Metadata
    MetricValue
    auPRC0.5549
    Calibrated Recall at 50% FDR0.233
    Number of Positive Examples in Test Data115692
    Number of Negative Examples in Test Data7955159
    Imbalance Ratio in Test Data0.0143
    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
Mbtps2
Fos
Hnf4g
Irf1
Pbx3
Ehf
Nfia
Sp3
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Hoxb9absent
Smarcc2absent
Hsf1absent
Klf1absent
Rfx8absent
Rfx1absent
Tcfecabsent
Grhl1absent
Creb3absent
Sp5absent
Foxa1absent
Foxp4absent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Hoxa11absent
Srebf2absent
Tcfcp2absent
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_263-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_263-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_263-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 23, # seqlets: 25865, Positive for: LRG_INTSTN;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_263-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_263-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_263-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 24, # seqlets: 11637, Negative for: LRG_INTSTN;8wks;D;En
  • pattern_0: # seqlets: 2604 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2538 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 2479 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Dbx1, Arid3b, Tlx2, Pou4f1, Sebox

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 907 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gli1, Gli2, Gli3, Zbtb7b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 722 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 342 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Nr1h2, Nr4a1, Esrrg, Nr4a3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 210 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Nfe2, Fos, Jund, Batf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 190 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 185 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hnf4g, Nr1h2, Pparg, Ppard, Nr6a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 173 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 173 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Klf1, Klf3, Klf8, Klf4, Klf2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 153 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut2, Foxd3, Onecut3, Onecut1, Foxm1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 122 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 120 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 92 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 108 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 86 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 83 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Bach1, Hnf4g, Rxra

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 73 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 64 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 61 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 53 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rfx1, Arid2, Rfx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 49 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 50 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores