In [1]:
# Parameters
sample_name = "MegP;A;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_193-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_193-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 01:09:32,817 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeMegakaryocyte progenitor cell
    Cell GroupOther Immune Cells
    Experiment NameATAC
    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
    rep117725912119515.04182869363376398130.266443879390.153127812600.4457
    rep217725912119515.66342876531879757000.277545307270.1576129009200.4488
    Modelling Metadata
    MetricValue
    auPRC0.6125
    Calibrated Recall at 50% FDR0.225
    Number of Positive Examples in Test Data140382
    Number of Negative Examples in Test Data7930469
    Imbalance Ratio in Test Data0.0174
    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
Creb3
Cebpb
Sfpi1
Bcl11a
Ctcf
Nfe2
Pbx3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Runx2absent
Mbtps2absent
Rfx2absent
Nfiaabsent
Restabsent
Sp3absent
Tcfebabsent
Mef2aabsent
Smarcc2absent
Elk3absent
Hsf1absent
Fevabsent
Gata6absent
Unique Homer Motifs
Motif NameModiscoHomer
Hmg20babsent
Zfp143absent
Gata2absent
Etv2absent
Sp2absent
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_193-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_193-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_193-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 24, # seqlets: 25858, Positive for: MegP;A;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_193-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_193-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_193-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 24, # seqlets: 10803, Negative for: MegP;A;En
  • pattern_0: # seqlets: 1889 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata6, Gata2, Gata5, Gata3, Gata4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1771 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1580 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 960 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 793 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 749 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7a, Sp3, Sp2, Wt1, Klf16

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 711 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut1, Onecut3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 360 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sfpi1, Bcl11a, Erg, Ets1, Spib

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 271 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tal1, Tcf21, Bhlha15, Neurog2, Neurog3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 242 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 224 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 210 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 143 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 123 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Cebpg, Cebpd, Cebpb, Cebpa, Cebpe

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 120 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 116 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 105 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx2, Runx1, Runx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 96 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Klf1, Klf4, Klf8, Klf12, Klf2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 78 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 70 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 63 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 36 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 59 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 34 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores