In [1]:
# Parameters
sample_name = "ILC2;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_86-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_86-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 19:28:02,630 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeILC2
    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
    rep11262959627914.10952962958582788800.279657290050.1935104601380.3533
    rep21262959627916.66181688819248755400.28937065090.219758963640.3495
    Modelling Metadata
    MetricValue
    auPRC0.5756
    Calibrated Recall at 50% FDR0.21
    Number of Positive Examples in Test Data110791
    Number of Negative Examples in Test Data7960060
    Imbalance Ratio in Test Data0.0137
    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
Pbx3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Ets1absent
Tcfecabsent
Mef2aabsent
9430076C15Rikabsent
Rfx1absent
Runx2absent
Nfiaabsent
Smarcc2absent
Tbpl2absent
Irf1absent
Relaabsent
Hsf1absent
Mbtps2absent
Nfe2absent
Gata2absent
Unique Homer Motifs
Motif NameModiscoHomer
Elk3absent
Zfp143absent
E4f1absent
Hes7absent
Smarcc1absent
Nfkb1absent
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_86-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_86-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_86-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 20, # seqlets: 21159, Positive for: ILC2;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_86-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_86-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_86-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 25, # seqlets: 6654, Negative for: ILC2;A;CL
  • pattern_0: # seqlets: 1760 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1219 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 674 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 598 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Nr4a1, Esrrg, Nr4a3, Nr4a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 200 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bhlha15

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 201 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 201 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 186 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rest

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 180 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 151 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 145 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Sp2, Zbtb7a, Wt1, Zfp281

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 133 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Maz, Bcl6, Sp1, E2f6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 126 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata4, Gata1, Gata2, Mecom, Gata6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 122 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zscan4c, Zscan4, Bhlha15, Tcf4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 114 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 106 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Wt1, Egr2, E2f1, Zfx

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 89 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 81 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Smarcc1, Fos, Batf, Nfe2l2, Fosb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 75 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 56 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 55 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, E2f1, Sp2, Tcfap2d, Zfx

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 47 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Maz, Zfp148, Rreb1, Klf15

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_24: # seqlets: 45 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rreb1, Maz, Zfp148, Sp3, Zfp281

    SequenceContrib ScoresHyp_Contrib Scores