In [1]:
# Parameters
sample_name = "wES;limb;E14.5;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_256-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_256-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 04:12:42,998 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typemixed embryonic mouse limb(E14.5)
    Cell GroupES cells and embryonic tissues
    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
    rep12395871509858.7845142677506204454070.1433124747160.0874557120840.3905
    rep223958715098510.328889941398126520280.140778849740.0877365792580.4068
    Modelling Metadata
    MetricValue
    auPRC0.6502
    Calibrated Recall at 50% FDR0.208
    Number of Positive Examples in Test Data130293
    Number of Negative Examples in Test Data7940558
    Imbalance Ratio in Test Data0.0161
    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
Tcfeb
Rfx1
Ctcf
Rest
Sp3
Pbx3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Creb3absent
Nficabsent
Hsf1absent
Tcf21absent
Erfabsent
Grhl1absent
Rfx8absent
Smarcc2absent
Mbtps2absent
Hoxd13absent
Nfixabsent
Sox3absent
Mef2dabsent
Nfatc1absent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Nfiaabsent
Ascl2absent
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_256-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_256-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_256-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 26, # seqlets: 22863, Positive for: wES;limb;E14.5;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_256-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_256-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_256-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 16, # seqlets: 9086, Negative for: wES;limb;E14.5;D;En
  • pattern_0: # seqlets: 2375 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Lcor

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1867 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Snai2, Zeb1, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1478 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp238, Tcf15, Tcf21, Bhlha15, Msc

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

    Nr2c1, Nr2f2, Rara, Nr2f6, Rarb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 715 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfic, Nfia, Nfix, Nfib, Hic1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 363 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pbx3, Foxi1, Nfya

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 230 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Nr5a2, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 205 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 144 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 132 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

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

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 90 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 85 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Trp73, Trp63, Tcfcp2l1, Grhl1, Tcfcp2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 56 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 37 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bach1, Fosb, Nfe2, Jund, Fosl1

    SequenceContrib ScoresHyp_Contrib Scores