In [1]:
# Parameters
sample_name = "B;B220_CD43;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_141-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_141-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 22:14:18,077 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeB220+CD43+ B cells
    Cell GroupB cells
    Experiment NameATAC
    Experiment GroupGEO
    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
    rep115584511905110.10669280898131162710.189482521720.1191247698330.3576
    rep215584511905111.25535162481189497660.173463521000.1231183211420.355
    Modelling Metadata
    MetricValue
    auPRC0.621
    Calibrated Recall at 50% FDR0.209
    Number of Positive Examples in Test Data130774
    Number of Negative Examples in Test Data7940077
    Imbalance Ratio in Test Data0.0162
    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
Sfpi1
Ebf1
Irf1
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Rfx1absent
Mef2aabsent
Fosabsent
Bcl11aabsent
Ergabsent
Hsf1absent
Creb3absent
Nfiaabsent
Pax5absent
Smarcc2absent
Foxi1absent
Sp3absent
Tcfecabsent
Jundabsent
Mbtps2absent
Ascl2absent
Runx2absent
Erfabsent
Gata6absent
Unique Homer Motifs
Motif NameModiscoHomer
Pbx3absent
Sp2absent
Atoh1absent
E4f1absent
Runx1absent
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_141-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_141-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_141-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 29, # seqlets: 26663, Positive for: B;B220_CD43;A;GEO
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_141-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_141-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_141-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 19, # seqlets: 7667, Negative for: B;B220_CD43;A;GEO
  • pattern_0: # seqlets: 1865 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Zbtb7b, Glis1, Zbtb7a, Zic5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1571 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Atoh8

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1495 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 510 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Stat5b, Nfkb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 471 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 444 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 239 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata5, Gata2, Gata6, Gata3, Gata4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 197 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1, Foxp4, Foxn3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 122 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hoxb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 119 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 103 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Spib

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 98 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 93 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) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 67 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Maz

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 53 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ebf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Sfpi1, Spib

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 33 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 56 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores