In [1]:
# Parameters
sample_name = "MN1;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_277-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_277-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 05:19:45,939 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeMN1 cell line
    Cell GroupCancer or Immortalized cells
    Experiment NameDHS
    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
    rep11828501341908.0448132797234210036130.1582127011990.0957484058210.3646
    rep218285013419020.8515917704318062650.197214431580.157634153330.373
    rep318285013419012.72545063990886956910.171862026100.1225186949360.3693
    rep418285013419016.105949368768145158660.294190081500.1825197897150.401
    rep518285013419036.325129818339168010.30958204380.276911684590.3944
    rep618285013419036.687621137345534590.26425833560.27858369720.3996
    rep718285013419021.2352527427779000360.312854586550.2161102951610.4077
    rep818285013419025.45461272152136907400.290629042360.228651457720.4051
    Modelling Metadata
    MetricValue
    auPRC0.5667
    Calibrated Recall at 50% FDR0.208
    Number of Positive Examples in Test Data152489
    Number of Negative Examples in Test Data7918362
    Imbalance Ratio in Test Data0.0189
    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
Nfia
Pbx3
Rfx1
Ctcf
Fos
Creb3
Prrxl1
Ebf1
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Atoh1absent
Irf1absent
Mbtps2absent
Sp3absent
Gata2absent
Smarcc2absent
Mef2dabsent
Erfabsent
Hand1absent
Hsf1absent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp637absent
Klf15absent
Zfp143absent
Klf5absent
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_277-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_277-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_277-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 22, # seqlets: 21262, Positive for: MN1;D;En
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_277-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_277-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_277-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 21, # seqlets: 8180, Negative for: MN1;D;En
  • pattern_0: # seqlets: 1953 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1536 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Zbtb7b, Glis1, Zic5, Zbtb7a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1074 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rfx2, Rest, Rfx1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 606 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata1, Gata4, Gata2, Gata6, Gata3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 516 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gli3, Zbtb7c, Gli1, Gli2, Hic2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 359 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: 325 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 253 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 174 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 166 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143, Myc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 149 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 140 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 111 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

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

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 87 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 76 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 75 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) :

    Fosb, Bach1, Jund, Smarcc1, Fosl1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 53 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores