In [1]:
# Parameters
sample_name = "ES;J1;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_98-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_98-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 20:06:37,874 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeJ1 embryonic stem cells
    Cell GroupES cells and embryonic tissues
    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
    rep1140739856598.91965403574965601880.121447712710.0883201020380.3721
    Modelling Metadata
    MetricValue
    auPRC0.6499
    Calibrated Recall at 50% FDR0.314
    Number of Positive Examples in Test Data83192
    Number of Negative Examples in Test Data7987659
    Imbalance Ratio in Test Data0.0103
    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
Klf5
Sox2
Gabpa
Pbx3
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Nfe2absent
Restabsent
Sox4absent
Rfx1absent
Tcfebabsent
Sp3absent
Tcfcp2l1absent
Creb3absent
Esrrbabsent
E2f1absent
Smarcc2absent
Unique Homer Motifs
Motif NameModiscoHomer
Mbd2absent
Sox13absent
Zfp143absent
Stat1absent
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_98-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_98-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_98-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 21, # seqlets: 19566, Positive for: ES;J1;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_98-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_98-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_98-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 15, # seqlets: 10669, Negative for: ES;J1;A;CL
  • pattern_0: # seqlets: 3039 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2843 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Dbx1, Arid3b, Tlx2, Pou4f1, Pit1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1606 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1595 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 335 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 316 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 301 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 106 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 104 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 91 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 72 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 74 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcfeb, Bach2, Tcfec, Mitf, Tcfe3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 68 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Myc, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 67 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pbx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 52 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores