In [1]:
# Parameters
sample_name = "DP3b;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_48-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_48-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 17:31:20,637 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeDN3b
    Cell GroupT 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
    rep1135393997539.203256525046101949660.180465348290.1156199684450.3534
    Modelling Metadata
    MetricValue
    auPRC0.582
    Calibrated Recall at 50% FDR0.247
    Number of Positive Examples in Test Data105288
    Number of Negative Examples in Test Data7965563
    Imbalance Ratio in Test Data0.013
    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
Klf16absent
Id4absent
Ergabsent
Smarcc2absent
Foxi1absent
Restabsent
Creb3absent
Nfiaabsent
Rfx1absent
Irf1absent
Lef1absent
Runx2absent
Sp2absent
Tbpl2absent
Tcfebabsent
Unique Homer Motifs
Motif NameModiscoHomer
Ets1absent
Pbx3absent
Sim1absent
Sp3absent
Zfp143absent
Tcf12absent
Tcf7l2absent
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_48-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_48-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_48-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 18, # seqlets: 23241, Positive for: DP3b;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_48-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_48-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_48-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 14, # seqlets: 11245, Negative for: DP3b;A;CL
  • pattern_0: # seqlets: 3211 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2936 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Dbx1, Arid3b, Tlx2, Pou4f1, Lhx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1764 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 709 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 676 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 433 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Ets1, ENSMUSG00000044690, Fev, Elf5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 425 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx2, Runx1, Runx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 279 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Fos, Smarcc1, Nfe2l2, Nfe2, Batf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 222 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 179 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 187 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 87 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata4, Gata1, Gata2, Mecom, Gata6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 100 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 37 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, Pitx3, Obox5, AC189028.1

    SequenceContrib ScoresHyp_Contrib Scores