In [1]:
# Parameters
sample_name = "ILC2precrsr;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_81-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_81-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 19:13:10,853 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeILC2 precursor
    Cell GroupOther Immune 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
    rep113506510992512.571646970013117549900.250476176090.1622155501220.3312
    Modelling Metadata
    MetricValue
    auPRC0.5847
    Calibrated Recall at 50% FDR0.207
    Number of Positive Examples in Test Data121656
    Number of Negative Examples in Test Data7949195
    Imbalance Ratio in Test Data0.0151
    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
Ctcf
Pbx3
Mbtps2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Smarcc2absent
Relbabsent
Sp3absent
Irf1absent
Nfixabsent
Hsf1absent
Creb1absent
Ets1absent
Ergabsent
Smarcc1absent
Gata4absent
Runx2absent
Rfx1absent
Tcfap2dabsent
Unique Homer Motifs
Motif NameModiscoHomer
Sp5absent
Hivep1absent
Gabpaabsent
Zfp143absent
Prdm1absent
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_81-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_81-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_81-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 19, # seqlets: 24006, Positive for: ILC2precrsr;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_81-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_81-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_81-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 21, # seqlets: 6339, Negative for: ILC2precrsr;A;CL
  • pattern_0: # seqlets: 1293 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Glis2, Glis1, Zbtb7a, Gli1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1178 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 612 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Twist1, Atoh8, Tcf4, Mesp2, Figla

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 581 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 502 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 349 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 240 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 238 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 206 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 183 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 164 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 162 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1, Runx2, Runx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 122 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 122 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1, Foxp4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 66 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 66 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 61 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 61 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox6, Sox12, Sox9, Sox4, Sox17

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 51 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Fosb, Bach1, Batf, Fos, Jund

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 37 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 45 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores