In [1]:
# Parameters
sample_name = "apCD4Eff;D;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_208-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_208-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.
2019-07-23 01:56:20,431 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeActivated primary CD4 effector cells, isolated ex vivo
    Cell GroupT cells
    Experiment NameDHS
    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
    rep1979527617510.57689807626192570610.2145129278770.144324359290.3612
    Modelling Metadata
    MetricValue
    auPRC0.6148
    Calibrated Recall at 50% FDR0.211
    Number of Positive Examples in Test Data91698
    Number of Negative Examples in Test Data7979153
    Imbalance Ratio in Test Data0.0114
    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
Pbx3
Ctcf
Mbtps2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Nfiaabsent
Tcf7l2absent
Fosabsent
Ets1absent
Gata2absent
Relaabsent
Irf1absent
Tcfebabsent
Rfx1absent
Sp3absent
Creb3absent
Smarcc2absent
Hsf1absent
Runx2absent
Lef1absent
Ergabsent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Prdm1absent
E4f1absent
Hivep1absent
Runx1absent
Etv5absent
Klf5absent
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_208-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_208-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_208-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 23, # seqlets: 25815, Positive for: apCD4Eff;D;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_208-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_208-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_208-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 16, # seqlets: 11363, Negative for: apCD4Eff;D;GEO
  • pattern_0: # seqlets: 3044 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Maz, Sp2, Plag1, Zbtb7a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2890 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Dbx1, Tlx2, Arid3b, Lhx3, Pou1f1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 2795 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 883 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hoxa9, Hoxb1, Hoxc9, Pbx2, Cdx4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 531 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcf4, Mesp2, Id4, Atoh8, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 365 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tal1, Bhlha15, Tcf15, Atoh8, Neurod1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 164 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 122 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 117 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Smarcc1, Fos, Nfe2l2, Fosb, Nfe2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 110 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 92 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 80 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 63 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 43 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 34 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 30 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores