In [1]:
# Parameters
sample_name = "STMCH;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_63-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_63-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 18:18:32,941 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typestomach
    Cell GroupOther Tissues
    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
    rep144310252149.228862556551277900.02053969660.063619513520.3129
    rep244310252146.91034694748014217160.030325372220.0541146693300.3126
    Modelling Metadata
    MetricValue
    auPRC0.6555
    Calibrated Recall at 50% FDR0.142
    Number of Positive Examples in Test Data28687
    Number of Negative Examples in Test Data8042164
    Imbalance Ratio in Test Data0.0036
    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
Mbtps2
Sp3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Ctcfabsent
Tcfebabsent
Grhl1absent
Elk3absent
Irf1absent
Rfx8absent
Klf16absent
Smarcc2absent
Gata2absent
Fosabsent
Nficabsent
Creb3absent
Nfiaabsent
Rfx2absent
Mef2babsent
Unique Homer Motifs
Motif NameModiscoHomer
Gabpaabsent
Sim1absent
Zfp143absent
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_63-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_63-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_63-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 24, # seqlets: 17616, Positive for: STMCH;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_63-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_63-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_63-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 18, # seqlets: 10021, Negative for: STMCH;A;CL
  • pattern_0: # seqlets: 2159 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Zbtb7a, Glis2, Glis1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1588 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gli3, Zbtb7c, Gli1, Gli2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1328 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1105 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Atoh8, Mesp2, Id4, Tcf4, Neurod1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 638 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 618 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rarb, Nr2f6, Rara, Nr2c1, Nr2f2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 566 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 555 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata2, Gata6, Gata1, Gata4, Gata5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 356 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 307 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 262 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 174 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 91 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1, Nr5a1, Sp3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 87 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Nr5a1, Esrrb, Sp3, Wt1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 55 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1, Nr5a1, Esr2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 42 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores