In [1]:
# Parameters
sample_name = "NPC;G4;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_171-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_171-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 23:54:39,091 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeneural progenitor cells(G4)
    Cell GroupNeural Cells and Tissues
    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
    rep12234431657346.8427148569741267343850.18129930080.0875576219070.3879
    Modelling Metadata
    MetricValue
    auPRC0.6077
    Calibrated Recall at 50% FDR0.237
    Number of Positive Examples in Test Data109057
    Number of Negative Examples in Test Data7961794
    Imbalance Ratio in Test Data0.0135
    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
Smarcc2
Pbx3
Ctcf
Creb3
Rfx1
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Myogabsent
Sp3absent
Restabsent
Nfiaabsent
Sox17absent
Erfabsent
Smarcc1absent
Tbpl2absent
Pou2f3absent
Stat2absent
Hsf1absent
Rfx8absent
Mbtps2absent
Mef2aabsent
Unique Homer Motifs
Motif NameModiscoHomer
Myod1absent
Sp5absent
Gabpaabsent
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_171-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_171-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_171-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 26, # seqlets: 20714, Positive for: NPC;G4;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_171-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_171-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_171-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 19, # seqlets: 12273, Negative for: NPC;G4;A;GEO
  • pattern_0: # seqlets: 2646 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b, Onecut1, Pit1, Arid3b, Onecut3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2461 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 2159 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rxrg, Rxrb, Nr2f2, Nr2f1, Rara

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1763 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 679 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata2, Gata1, Gata4, Gata6, Gata5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 610 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 327 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 287 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 265 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Maz, Rreb1, Sp3, Zfp281, Zfp148

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 178 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 161 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hoxc9, Hoxd9, Hoxa9, Cdx4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 126 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 108 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gli1, Gli3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 92 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1, Nr5a1, Esr2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 94 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Nr5a2, Smarcc2, Nr6a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 89 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Plagl1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 113 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 59 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

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

    SequenceContrib ScoresHyp_Contrib Scores