In [1]:
# Parameters
sample_name = "wCH12_drug;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_93-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_93-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 19:53:20,618 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typech12 wt with drug
    Cell GroupCancer or Immortalized 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
    rep12133471744614.9591207358221NANANANANANA
    Modelling Metadata
    MetricValue
    auPRC0.5027
    Calibrated Recall at 50% FDR0.275
    Number of Positive Examples in Test Data71696
    Number of Negative Examples in Test Data7999155
    Imbalance Ratio in Test Data0.0089
    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
Creb3
Tcfec
Tbpl2
Bcl11a
Pbx3
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Runx2absent
Batfabsent
Relbabsent
Smarcc2absent
Mef2aabsent
Ebf1absent
Sp3absent
Klf16absent
Elk3absent
Ascl2absent
Rfx1absent
Nfat5absent
Mbtps2absent
Irf1absent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Klf5absent
Sfpi1absent
Fosabsent
Nfkb1absent
Yy1absent
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_93-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_93-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_93-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 23, # seqlets: 23991, Positive for: wCH12_drug;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_93-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_93-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_93-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 22, # seqlets: 7321, Negative for: wCH12_drug;A;CL
  • pattern_0: # seqlets: 2061 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b, Onecut1, Phf21a, Pit1, Dbx1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1432 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Snai2, Zeb1, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 983 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Glis2, Glis1, Zbtb7a, Zic5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 737 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Myc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 571 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 236 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rela

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 127 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 125 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Zfx, Zbtb7a, E2f1, Mtf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 109 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 108 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 100 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 96 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Smarcc1, Fos, Batf, Bach1, Nfe2l2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 83 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1, Runx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 81 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 80 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tbpl2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 78 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 79 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 62 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Myc, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 48 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 47 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Myc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 41 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 37 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Zfx, Tcfap2d, E2f1, Zbtb7a

    SequenceContrib ScoresHyp_Contrib Scores