In [1]:
# Parameters
sample_name = "ES;E14;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_50-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_50-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 17:36:15,364 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeES cells (E14)
    Cell GroupES cells and embryonic 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
    rep117933610612710.43514572177077903220.170544904510.0983182848310.4001
    Modelling Metadata
    MetricValue
    auPRC0.5586
    Calibrated Recall at 50% FDR0.252
    Number of Positive Examples in Test Data116933
    Number of Negative Examples in Test Data7953918
    Imbalance Ratio in Test Data0.0145
    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
Pbx3
Pou5f1
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Klf2absent
Restabsent
Smarcc2absent
Fosabsent
Sox9absent
Tcfecabsent
Erfabsent
Jdp2absent
Esrrgabsent
Rfx2absent
Rfx5absent
Sp3absent
Lef1absent
Tcfcp2l1absent
Unique Homer Motifs
Motif NameModiscoHomer
E4f1absent
Sox2absent
Zfp143absent
Klf5absent
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_50-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_50-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_50-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 23, # seqlets: 20777, Positive for: ES;E14;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_50-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_50-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_50-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 18, # seqlets: 12916, Negative for: ES;E14;A;CL
  • pattern_0: # seqlets: 2622 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b, Dbx1, Pit1, Pou4f3, Tlx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2464 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 2198 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp740, Zbtb7b, Zfp202, Glis3, Zfp219

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1256 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 917 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 906 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 638 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid5a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 404 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ets1, Erg, Fev, ENSMUSG00000044690, Elf5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 373 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gm98

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 290 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Hsf1, Nr6a1, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 216 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 157 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 103 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

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

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 80 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 61 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 58 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxi1, Pbx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 88 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores