In [1]:
# Parameters
sample_name = "MegEP;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_191-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_191-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 01:04:00,806 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeMegakaryocyte-erythroid progenitor cell
    Cell GroupOther Immune Cells
    Experiment NameATAC
    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
    rep1120903797428.44933675378140475570.110237284380.1015136916840.3727
    rep2120903797429.05023570105645996480.128938543720.108133835610.3751
    Modelling Metadata
    MetricValue
    auPRC0.5575
    Calibrated Recall at 50% FDR0.243
    Number of Positive Examples in Test Data91857
    Number of Negative Examples in Test Data7978994
    Imbalance Ratio in Test Data0.0114
    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
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Elk3absent
Nfe2absent
Rfx2absent
Creb3absent
Klf2absent
Rfx8absent
Sp3absent
Mbtps2absent
Tcfebabsent
Restabsent
Gata6absent
Smarcc2absent
Hsf1absent
Irf1absent
Nfiaabsent
Unique Homer Motifs
Motif NameModiscoHomer
Gata4absent
Zfp143absent
E4f1absent
Elk1absent
Sp5absent
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_191-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_191-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_191-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 19, # seqlets: 22021, Positive for: MegEP;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_191-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_191-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_191-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 15, # seqlets: 9527, Negative for: MegEP;A;CL
  • pattern_0: # seqlets: 1760 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1569 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Sp2, Zbtb7a, Rreb1, Maz

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1444 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1162 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 901 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata6, Gata2, Gata4, Gata5, Gata3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 807 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 649 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gli3, Gli2, Gli1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 594 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Stat5b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 231 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 95 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 71 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 85 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 82 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 39 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Klf1, Klf4, Klf8, Klf12, Klf2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 38 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores