In [1]:
# Parameters
sample_name = "NCR+ILC3;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_82-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_82-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 19:16:18,528 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeNCR+ILC3
    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
    rep112435210265611.390758606297148747250.253987277060.149197557890.3372
    Modelling Metadata
    MetricValue
    auPRC0.5465
    Calibrated Recall at 50% FDR0.244
    Number of Positive Examples in Test Data117538
    Number of Negative Examples in Test Data7953313
    Imbalance Ratio in Test Data0.0146
    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
Rela
Sp3
Mbtps2
Rorc
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Jdp2absent
Runx1absent
Nfiaabsent
Rfx8absent
Smarcc2absent
Rfx1absent
Gata2absent
Irf1absent
Bach2absent
Fosabsent
Ergabsent
Ets1absent
Unique Homer Motifs
Motif NameModiscoHomer
Smarcc1absent
E4f1absent
Gabpaabsent
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_82-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_82-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_82-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 21, # seqlets: 22673, Positive for: NCR+ILC3;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_82-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_82-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_82-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 16, # seqlets: 6257, Negative for: NCR+ILC3;A;CL
  • pattern_0: # seqlets: 1529 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Zbtb7a, Glis2, Glis1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1117 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Mga, Tcf4, Tbx4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 929 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Esrra, Esrrg, Nr4a2, Nr2f6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 563 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox9, Sox17, Sox6, Sox2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 553 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 334 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hic1, Hic2, Nfic, Nfia, Nfib

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 267 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ets1, Erg, ENSMUSG00000044690, Etv6, Etv5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 256 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 252 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 137 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 102 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 49 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Myc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 45 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 41 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) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 37 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores