In [1]:
# Parameters
sample_name = "DP3a;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_47-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_47-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 17:28:35,841 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeDN3a
    Cell GroupT 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
    rep115465211598611.88944152129498457690.237254800600.132154010780.3711
    Modelling Metadata
    MetricValue
    auPRC0.5771
    Calibrated Recall at 50% FDR0.238
    Number of Positive Examples in Test Data126544
    Number of Negative Examples in Test Data7944307
    Imbalance Ratio in Test Data0.0157
    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
Erg
Pbx3
Smarcc2
Irf1
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Hsf1absent
Creb3absent
Restabsent
Mbtps2absent
Tcfecabsent
Runx2absent
Nfe2l2absent
Nfiaabsent
Ets1absent
Gata2absent
Sp3absent
Rfx1absent
Unique Homer Motifs
Motif NameModiscoHomer
Sp2absent
Myogabsent
Bach2absent
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_47-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_47-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_47-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 20, # seqlets: 23978, Positive for: DP3a;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_47-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_47-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_47-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 16, # seqlets: 7743, Negative for: DP3a;A;CL
  • pattern_0: # seqlets: 2093 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Sp2, E2f1, Zbtb7a, Wt1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1823 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut1, Onecut3, Arid3b, Onecut2, Hmg20b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1242 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Tcf4, Tcf3, Mga

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 870 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 484 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bhlha15, Msc, Tcf21, Twist2, Tcf15

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 361 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 186 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 159 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 146 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Klf1, Klf2, Klf8, Klf4, Klf12

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 65 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 62 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Fev, ENSMUSG00000044690, Erg

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 61 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 47 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 54 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores