In [1]:
# Parameters
sample_name = "DC_LPS;6h;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_146-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_146-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 22:30:30,585 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typedendritic cell(100 ng/mL Lipopolysaccharide, 6hours)
    Cell GroupOther Immune Cells
    Experiment NameATAC
    Experiment GroupGEO
    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
    rep118076512853712.070553928405167347040.310486684980.1608227483040.422
    Modelling Metadata
    MetricValue
    auPRC0.6393
    Calibrated Recall at 50% FDR0.203
    Number of Positive Examples in Test Data154075
    Number of Negative Examples in Test Data7916776
    Imbalance Ratio in Test Data0.0191
    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
Mbtps2
Sp3
Sfpi1
Fos
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Nfiaabsent
9430076C15Rikabsent
Hsf1absent
Runx1absent
Restabsent
Ets1absent
Tcfecabsent
Klf16absent
Smarcc2absent
Tbpl2absent
Bcl11aabsent
Gabpaabsent
Elk1absent
Nfkb1absent
Foxi1absent
Rfx2absent
Runx2absent
Mef2aabsent
Cebpbabsent
Unique Homer Motifs
Motif NameModiscoHomer
Relaabsent
Cebpdabsent
Tefabsent
Irf4absent
Zfp143absent
Pbx3absent
Sohlh2absent
Tcfebabsent
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_146-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_146-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_146-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 26, # seqlets: 26401, Positive for: DC_LPS;6h;A;GEO
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_146-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_146-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_146-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 20, # seqlets: 11028, Negative for: DC_LPS;6h;A;GEO
  • pattern_0: # seqlets: 1853 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Snai2, Zeb1, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1388 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b, Onecut1, Onecut3, Dbx1, Phf21a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1325 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1264 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b, Dbx1, Lhx3, Arid3b, Pit1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 1202 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Klf15, Maz, Rreb1, Sp2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 1126 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 506 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Nfe2, Jund, Batf, Fos

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 497 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gli1, Gli2, Gli3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 317 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 276 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Esrrg, Rarb, Nr4a1, Rxra

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 233 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 194 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 188 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Cebpd, Cebpg, Cebpb, Cebpe, Cebpa

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 152 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Egr2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 108 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 103 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 84 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Egr2, Hif3a, Rreb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 84 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 67 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Hsf1, Nr6a1, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 61 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rest, Gli2

    SequenceContrib ScoresHyp_Contrib Scores