In [1]:
# Parameters
sample_name = "Mammary_GLND;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_103-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_103-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 20:23:16,174 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeMammary Gland(WT,Basal Mammary Epithelial Cells)
    Cell GroupOther Tissues
    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
    rep119145613986322.05022099256066350130.316338478790.183587526690.4173
    rep219145613986325.297869898528158870.324318530960.213435938380.414
    rep319145613986316.27153283877180966020.246747902720.146128247060.3908
    rep419145613986315.666743058729120143620.279164476980.1498175180800.407
    rep519145613986310.36092944289818322230.062319286210.065594646650.3217
    Modelling Metadata
    MetricValue
    auPRC0.6575
    Calibrated Recall at 50% FDR0.195
    Number of Positive Examples in Test Data176806
    Number of Negative Examples in Test Data7894045
    Imbalance Ratio in Test Data0.0219
    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
Gabpa
Rela
Fos
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Srfabsent
Runx2absent
Tcfap2aabsent
Rfx1absent
Cebpbabsent
Sp3absent
Batf3absent
Trp73absent
Smarcc2absent
Mbtps2absent
E2f1absent
Sox17absent
Creb1absent
Nfiaabsent
Irf1absent
Foxi1absent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Creb3absent
Pbx3absent
Sp2absent
Cebpgabsent
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_103-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_103-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_103-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 22, # seqlets: 18203, Positive for: Mammary_GLND;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_103-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_103-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_103-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 22, # seqlets: 13291, Negative for: Mammary_GLND;A;GEO
  • pattern_0: # seqlets: 2591 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Zbtb7b, Glis1, Zbtb7a, Zic5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1636 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Phf21a, Onecut1, Pit1, Arid3b, Foxl1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1404 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1056 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 988 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 699 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata2, Gata4, Gata1, Mecom, Gata6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 648 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 580 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rarb, Ppara, Rara, Nr2f6, Rxra

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 538 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 521 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 476 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut1, Onecut3, Onecut2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 369 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcfap2a, Tcfap2c

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 289 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Nfe2, Jund, Batf, Fos

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 261 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfic

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 255 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Mesp2, Id4, Tcf4, Myf6, Atoh8

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 232 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 226 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ets1, Etv6, Elk1, Fli1, Etv3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 198 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 124 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Obox5, Pitx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 87 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1, Nr5a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 49 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 64 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores