In [1]:
# Parameters
sample_name = "Hnd_BRN;P0;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_247-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_247-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 03:45:05,528 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typemixed mouse hindbrain(P0)
    Cell GroupNeural Cells and 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
    rep124969716402110.1766142326235255773550.1797137807380.0968594554600.4178
    rep22496971640219.8996123297728182903300.1484112868420.0916470007310.3813
    Modelling Metadata
    MetricValue
    auPRC0.684
    Calibrated Recall at 50% FDR0.193
    Number of Positive Examples in Test Data141568
    Number of Negative Examples in Test Data7929283
    Imbalance Ratio in Test Data0.0175
    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
Sp3
Gabpa
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Neurod1absent
Pbx3absent
Sox3absent
Zfp281absent
Ebf1absent
Lhx2absent
Mef2cabsent
Hsf1absent
Zic1absent
Rfx1absent
Nfiaabsent
E2f1absent
Smarcc2absent
Tcfecabsent
9430076C15Rikabsent
Mbtps2absent
Unique Homer Motifs
Motif NameModiscoHomer
Rfx2absent
Gbx1absent
Lmx1aabsent
Stat1absent
Tal1absent
Zfp740absent
Zfp143absent
Arntlabsent
E2f8absent
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_247-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_247-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_247-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 21, # seqlets: 18884, Positive for: Hnd_BRN;P0;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_247-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_247-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_247-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 21, # seqlets: 9016, Negative for: Hnd_BRN;P0;D;En
  • pattern_0: # seqlets: 1693 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Snai2, Zeb1, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1126 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1087 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Myt1l

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 952 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 932 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b, Phf21a, Pit1, Onecut1, Dbx1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 587 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut1, Onecut3, Onecut2, Cux2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 510 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp238, Tcf15, Tcf21, Bhlha15, Msc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 392 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 295 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 255 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata2, Gata4, Gata1, Mecom, Gata6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 222 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Fos, Nfe2, Jund, Batf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 186 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 142 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 115 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 117 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfic

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 90 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

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

    Pitx2, AC189028.1, Pitx3, Nr5a2, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 76 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 73 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 40 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1, Nr5a1

    SequenceContrib ScoresHyp_Contrib Scores