In [1]:
# Parameters
sample_name = "ILC2_AbxGRMFree;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_111-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_111-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 20:47:36,808 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeILC2_AbxGermFree
    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
    rep11193968830812.63872347235624091080.102722495470.095980026010.3412
    rep21193968830815.08582084428566628870.319943337700.208180852550.3882
    Modelling Metadata
    MetricValue
    auPRC0.584
    Calibrated Recall at 50% FDR0.184
    Number of Positive Examples in Test Data97973
    Number of Negative Examples in Test Data7972878
    Imbalance Ratio in Test Data0.0121
    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
Pbx3
Rela
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Gata2absent
Hsf1absent
Rfx2absent
Runx2absent
Ergabsent
Jdp2absent
Fosbabsent
Tcfebabsent
Sp3absent
Smarcc2absent
Nfiaabsent
Irf1absent
Tbpl2absent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Sp5absent
Runx3absent
Elk1absent
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_111-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_111-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_111-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 23, # seqlets: 25057, Positive for: ILC2_AbxGRMFree;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_111-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_111-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_111-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 29, # seqlets: 11769, Negative for: ILC2_AbxGRMFree;A;GEO
  • pattern_0: # seqlets: 1437 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Tcf4, Mga, Mesp2, Tbx4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1293 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Glis1, Zbtb7b, Zbtb7a, Zic5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1276 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Dbx1, Tlx2, Arid3b, Sebox, Pou4f1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1273 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Maz, Zfp148, Zfp281, Sp2, Sp3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 1235 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rfx1, Arid2, Rfx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 797 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata6, Gata5, Gata2, Gata4, Gata3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 612 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 537 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Esrra

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 493 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox9, Sox6, Sox17

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 489 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7c, Gli3, Gli1, Gli2, Hic2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 377 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bhlhe23, Olig1, Olig2, Twist2, Neurod2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 196 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 184 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hoxb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 156 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

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

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 131 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5, Otx1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 113 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 107 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut2, Runx2, Foxd3, Rreb1, Onecut3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 117 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 107 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Myc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 101 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 89 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 86 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Egr2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 85 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_24: # seqlets: 78 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_25: # seqlets: 76 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Jund, Nfe2, Fosb, Batf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_26: # seqlets: 78 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_27: # seqlets: 52 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_28: # seqlets: 48 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores