In [1]:
# Parameters
sample_name = "wCH12;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_91-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_91-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 19:46:31,287 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typech12 wt
    Cell GroupCancer or Immortalized 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
    rep1942266167012.47372867910332883640.114731919410.111498599010.344
    rep2942266167015.88562160800632039410.148429853640.138375327650.3489
    Modelling Metadata
    MetricValue
    auPRC0.5868
    Calibrated Recall at 50% FDR0.23
    Number of Positive Examples in Test Data66776
    Number of Negative Examples in Test Data8004075
    Imbalance Ratio in Test Data0.0083
    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
Sfpi1
Ctcf
Runx2
Mbtps2
Tbpl2
Pbx3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Bcl11aabsent
Rfx1absent
Fosabsent
Ets1absent
Ebf1absent
Relbabsent
Klf16absent
Mef2aabsent
Tcfecabsent
Smarcc2absent
Hsf1absent
Gabpaabsent
Sp3absent
Zfp281absent
Jdp2absent
Mef2babsent
Unique Homer Motifs
Motif NameModiscoHomer
Rfx7absent
Relaabsent
E4f1absent
Klf5absent
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_91-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_91-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_91-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 24, # seqlets: 24452, Positive for: wCH12;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_91-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_91-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_91-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 27, # seqlets: 6897, Negative for: wCH12;A;CL
  • pattern_0: # seqlets: 1837 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1304 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Glis2, Glis1, Zbtb7a, Zic5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1158 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Scrt1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 369 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 291 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 199 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 173 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 156 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tal1, Atoh1, Neurod1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 140 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 125 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 112 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hif3a, Egr2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 109 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 87 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) :

    Maz, Sp3, Wt1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 85 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Jund, Smarcc1, Fosb, Batf, Junb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 76 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rreb1, Egr2, Smad2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 80 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 69 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 62 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 49 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 52 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 49 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 63 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 45 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_24: # seqlets: 43 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rfx1, Rfx2, Arid2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_25: # seqlets: 42 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_26: # seqlets: 37 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores