In [1]:
# Parameters
sample_name = "DC_BMD;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_43-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_43-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 17:16:06,732 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeBMDCs(dendritic cell)
    Cell GroupOther Immune Cells
    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
    rep117200212448114.69721995829965875930.330438068150.190983839250.4205
    rep217200212448118.763427423912107955410.393960444680.2206124482910.4542
    Modelling Metadata
    MetricValue
    auPRC0.6392
    Calibrated Recall at 50% FDR0.206
    Number of Positive Examples in Test Data150516
    Number of Negative Examples in Test Data7920335
    Imbalance Ratio in Test Data0.0186
    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
Sfpi1
Sp3
Irf1
Runx2
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Mbtps2absent
Nfkb1absent
Hsf1absent
Arid2absent
Mef2babsent
Smarcc2absent
Foxi1absent
Fosabsent
Tcfecabsent
Nfixabsent
9430076C15Rikabsent
Erfabsent
Cebpbabsent
Unique Homer Motifs
Motif NameModiscoHomer
Yy1absent
Cebpdabsent
Ybx1absent
Zfp143absent
Sohlh2absent
Nr2f6absent
Nfe2l2absent
Relaabsent
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_43-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_43-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_43-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 20, # seqlets: 27433, Positive for: DC_BMD;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_43-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_43-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_43-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 24, # seqlets: 9427, Negative for: DC_BMD;A;CL
  • pattern_0: # seqlets: 1934 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Zbtb7a, Glis2, Glis1, Zic5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1627 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1568 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Dbx1, Tlx2, Arid3b, Sebox, Pou4f1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 935 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 656 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr4a3, Nr4a1, Ppara, Nr1h2, Ppard

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 339 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 315 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gli3, Gli1, Gli2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 269 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Nfe2, Jund, Fos, Batf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 243 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 191 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 187 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Stat5b, Nfkb1, Rela

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 160 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 128 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 104 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Cebpd, Cebpg, Cebpb, Cebpe, Cebpa

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 103 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Mtf1, Zfx, Wt1, E2f1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 97 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 83 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfkb1, Rel, Rela, Relb, Hivep1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 83 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 82 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 77 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rel, Nfkb1, Hivep1, Relb, Rela

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 74 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 65 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 65 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf

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

    SequenceContrib ScoresHyp_Contrib Scores