In [1]:
# Parameters
sample_name = "B_SPLND;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_139-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_139-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 22:09:00,835 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeSplenic B cell
    Cell GroupB 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
    rep152733325688.18482480668213880180.05619173920.077480120420.3232
    rep252733325687.1682911867614549310.0521158430.072793024650.3197
    Modelling Metadata
    MetricValue
    auPRC0.6035
    Calibrated Recall at 50% FDR0.222
    Number of Positive Examples in Test Data40505
    Number of Negative Examples in Test Data8030346
    Imbalance Ratio in Test Data0.005
    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
Sfpi1
Ctcf
Pbx3
Tbpl2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Nfkb1absent
Mbtps2absent
Ebf1absent
Bcl11aabsent
Rfx8absent
Rfx2absent
Atf7absent
Smarcc2absent
Ets1absent
Tcfecabsent
Gmeb2absent
Sp3absent
Gabpaabsent
Unique Homer Motifs
Motif NameModiscoHomer
Irf1absent
Klf1absent
Tcfap2dabsent
Fosl2absent
Klf13absent
Mycnabsent
Yy1absent
Klf5absent
Zfp143absent
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_139-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_139-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_139-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 20, # seqlets: 24624, Positive for: B_SPLND;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_139-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_139-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_139-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 12, # seqlets: 8242, Negative for: B_SPLND;A;GEO
  • pattern_0: # seqlets: 1751 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Dbx1, Tlx2, Arid3b, Pou4f1, Lhx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1730 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Atoh8, Tcf4, Snai2, Twist1, Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1599 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfkb1, Stat5b, Tbx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1307 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7a, Zbtb7b, Glis1, Glis2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 856 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 543 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid5a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 102 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 99 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 87 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 80 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 45 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 43 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores