In [1]:
# Parameters
sample_name = "B1_B;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_10-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_10-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 15:35:33,116 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeB1 B cells
    Cell GroupB 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
    rep11072388407613.80314651015777132000.165952558440.1131147288400.3168
    Modelling Metadata
    MetricValue
    auPRC0.5533
    Calibrated Recall at 50% FDR0.225
    Number of Positive Examples in Test Data87013
    Number of Negative Examples in Test Data7983838
    Imbalance Ratio in Test Data0.0108
    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
Common Motifs
Motif NameModiscoHomer
Mbtps2
Sfpi1
Pbx3
Tbpl2
Sp3
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Smarcc2absent
Fosabsent
Jdp2absent
Bcl11aabsent
Tcfebabsent
Etv2absent
Ets1absent
Hsf1absent
Rfx1absent
Runx1absent
Relbabsent
Unique Homer Motifs
Motif NameModiscoHomer
E4f1absent
Zfp143absent
Relaabsent
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_10-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_10-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_10-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 21, # seqlets: 23658, Positive for: B1_B;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_10-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_10-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_10-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 20, # seqlets: 6447, Negative for: B1_B;A;CL
  • pattern_0: # seqlets: 2281 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Glis1, Glis2, Zbtb7a, Gli1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1062 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Mesp2, Zeb1, Snai2, Id4, Tcf4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 745 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 534 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox17, Sox6, Sox9, Sox2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 252 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Pitx2, AC189028.1, Esr2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 196 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 195 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tbpl2, Lin54

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 189 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 186 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 142 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Myc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 119 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 111 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1, Nr5a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 90 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hif3a, Egr2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 85 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 51 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 47 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1, Esr2, Nr5a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 45 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 39 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 32 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr6a1, Nr5a1, Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores