In [1]:
# Parameters
sample_name = "ES;E14;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_217-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_217-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 02:14:59,970 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typemouse embryonic stem cells E14
    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
    rep119422012813714.27093182036980025210.251646927290.1476135056310.4247
    rep21942201281379.2692292554325446540.111123080870.100889255420.3897
    Modelling Metadata
    MetricValue
    auPRC0.6432
    Calibrated Recall at 50% FDR0.178
    Number of Positive Examples in Test Data139855
    Number of Negative Examples in Test Data7930996
    Imbalance Ratio in Test Data0.0173
    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
Klf5
Tcfeb
Sox2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Smarcc2absent
Pou5f1absent
Hsf1absent
Zic4absent
Rfx8absent
Sp3absent
Rfx1absent
Gabpaabsent
E2f1absent
Sp2absent
Restabsent
Nr6a1absent
Foxi1absent
Mbtps2absent
Tcfcp2l1absent
Nfe2l2absent
Unique Homer Motifs
Motif NameModiscoHomer
Elf1absent
Esrrgabsent
Zfp143absent
Pbx3absent
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_217-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_217-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_217-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 30, # seqlets: 25923, Positive for: ES;E14;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_217-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_217-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_217-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 13, # seqlets: 12193, Negative for: ES;E14;D;En
  • pattern_0: # seqlets: 3425 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Phf21a, Pit1, Onecut1, Arid3b, Hmg20b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 3064 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1935 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rreb1, Sp3, Zbtb7a, Zfp281, Klf16

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1717 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 977 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 378 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 172 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Fos, Bach1, Smarcc1, Nfe2, Fosb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 164 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 104 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Maz, Plag1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 86 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 83 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 48 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Maz

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 40 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores