In [1]:
# Parameters
sample_name = "ILC2;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_108-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_108-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 20:37:49,015 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeILC2(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
    rep11258149619415.04972396084466560330.27841846840.174895973740.4008
    rep21258149619417.09492200491846757480.212732276400.146883942490.3818
    Modelling Metadata
    MetricValue
    auPRC0.5957
    Calibrated Recall at 50% FDR0.196
    Number of Positive Examples in Test Data106509
    Number of Negative Examples in Test Data7964342
    Imbalance Ratio in Test Data0.0132
    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
Irf1
Mbtps2
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Smarcc2absent
Fosabsent
Rfx1absent
Ets1absent
Sp3absent
Tbpl2absent
Hsf1absent
Nfiaabsent
Ergabsent
Runx2absent
Gata2absent
9430076C15Rikabsent
Relaabsent
Tcfebabsent
Foxi1absent
Rfx8absent
Unique Homer Motifs
Motif NameModiscoHomer
Pbx3absent
Smarcc1absent
Tbx2absent
Hivep1absent
Pax9absent
E2f3absent
Klf16absent
Erfabsent
E2f1absent
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_108-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_108-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_108-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 24, # seqlets: 24789, Positive for: ILC2;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_108-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_108-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_108-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 30, # seqlets: 9399, Negative for: ILC2;A;GEO
  • pattern_0: # seqlets: 1029 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Rreb1, Zfp281, Sp2, Zfp148

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1007 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b, Zfp637, Hmg20b, Ahctf1, Tbp

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 938 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 754 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Scrt1, Id4, Mesp2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 536 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcf15, Tal1, Msc, Neurod2, Neurog1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 521 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hic2, Gli3, Gli2, Gli1, Hic1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 446 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox9, Sox17, Sox6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 437 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Nr1h2, Esrrg, Nr4a2, Nr1i3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 346 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 305 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 286 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b, Phf21a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 280 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 272 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b, Onecut3, Phf21a, Onecut1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 255 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Uncx, Lhx1, Shox2, Alx3, Alx4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 231 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Nfe2, Fos, Jund, Smarcc1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 209 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 209 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 163 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 157 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 144 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b, Ahctf1, Onecut1, Tbp, Arid3b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 140 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b, Arid3b, Zfp637, Onecut1, Phf21a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 135 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 131 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b, Tbp, Ahctf1, Zfp637, Phf21a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 128 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_24: # seqlets: 75 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Zbtb7a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_25: # seqlets: 68 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_26: # seqlets: 65 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_27: # seqlets: 55 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b, Arid3b, Onecut1, Pit1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_28: # seqlets: 43 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_29: # seqlets: 34 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1

    SequenceContrib ScoresHyp_Contrib Scores