In [1]:
# Parameters
sample_name = "ILC3;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_109-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_109-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 20:41:52,988 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeILC3(WT)
    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
    rep114195710958013.86433112855586893120.279350046490.1609125426060.4032
    rep214195710958013.14773255446764551280.198444324970.1362125046050.3843
    Modelling Metadata
    MetricValue
    auPRC0.6104
    Calibrated Recall at 50% FDR0.192
    Number of Positive Examples in Test Data123152
    Number of Negative Examples in Test Data7947699
    Imbalance Ratio in Test Data0.0153
    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
Irf1
Smarcc2
Pbx3
Erg
Rorc
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Tbpl2absent
Runx1absent
Gata2absent
Relaabsent
Nfiaabsent
Creb3absent
Fosabsent
Rfx8absent
Ets1absent
Rfx1absent
Mbtps2absent
Klf16absent
Tcfebabsent
Unique Homer Motifs
Motif NameModiscoHomer
Tcfecabsent
Smarcc1absent
Runx2absent
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_109-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_109-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_109-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 22, # seqlets: 22523, Positive for: ILC3;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_109-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_109-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_109-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 22, # seqlets: 5584, Negative for: ILC3;A;GEO
  • pattern_0: # seqlets: 1076 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Zbtb7a, Glis1, Zbtb7b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 833 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Zbtb7a, Rreb1, Zfp148, Sp3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 732 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 681 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Scrt1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 664 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gli1, Gli2, Gli3, Zbtb7b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 346 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rarb, Ppara, Rxra, Nr2f6, Rara

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 130 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut1, Onecut3, Cux2, Onecut2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 117 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Cux2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 113 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 107 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Nfe2, Smarcc1, Jund, Fos

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 93 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 91 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 81 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Sfpi1, Spib, Irf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 75 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 76 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 70 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Irf1, Sfpi1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 61 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 62 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1, Nr5a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 54 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 48 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Sfpi1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 30 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Spic, Spib, Bcl11a, Sfpi1

    SequenceContrib ScoresHyp_Contrib Scores