In [1]:
# Parameters
sample_name = "Muscle;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_55-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_55-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 17:52:59,316 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeMuscle
    Cell GroupOther Tissues
    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
    rep1100569700578.45526551867784594190.129263026490.0962237312420.3623
    Modelling Metadata
    MetricValue
    auPRC0.6301
    Calibrated Recall at 50% FDR0.212
    Number of Positive Examples in Test Data69117
    Number of Negative Examples in Test Data8001734
    Imbalance Ratio in Test Data0.0086
    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
Sp3
Ctcf
Pbx3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Creb1absent
Smarcc2absent
Nr4a3absent
Nfiaabsent
Cebpbabsent
Irf1absent
Fosbabsent
Rfx8absent
Mbtps2absent
Elk3absent
Nr3c1absent
Ascl2absent
Mef2dabsent
Unique Homer Motifs
Motif NameModiscoHomer
Mef2babsent
Gabpaabsent
Zfp143absent
Tcf12absent
Cremabsent
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_55-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_55-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_55-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 25, # seqlets: 20385, Positive for: Muscle;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_55-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_55-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_55-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 25, # seqlets: 11753, Negative for: Muscle;A;CL
  • pattern_0: # seqlets: 1952 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1700 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Zbtb7a, Zbtb7b, Glis1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1594 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1327 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 1112 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox17, Sox6, Sox2, Sox9, Sox3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 661 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tbp, Hmg20b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 588 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 535 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gli1, Gli3, Gli2, Zbtb7b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 387 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rfx1, Arid2, Rfx2, Rfx4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 305 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 206 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 189 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 174 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfic

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 171 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 146 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rxra, Ppara, Nr1i3, Nr1h2, Thrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 128 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata4, Gata1, Gata2, Mecom, Gata6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 103 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, E2f3, Hic2, Zscan4, E2f1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 99 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 84 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 72 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Esr2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 54 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bhlha15

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

    Ctcf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 42 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_24: # seqlets: 31 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores