In [1]:
# Parameters
sample_name = "aB_CD40+IL4;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_17-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_17-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 15:58:32,791 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeaB aCD40+IL4
    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
    rep1625734314510.67358229649369883130.084968722360.0835262529200.3191
    Modelling Metadata
    MetricValue
    auPRC0.7064
    Calibrated Recall at 50% FDR0.157
    Number of Positive Examples in Test Data43501
    Number of Negative Examples in Test Data8027350
    Imbalance Ratio in Test Data0.0054
    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
Tbpl2
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Mbtps2absent
Mef2aabsent
Relabsent
Sp2absent
Bcl11aabsent
Rfx1absent
Sp3absent
Etv6absent
Smarcc2absent
Jdp2absent
Hsf1absent
Foxi1absent
Smarcc1absent
Tcfebabsent
Unique Homer Motifs
Motif NameModiscoHomer
Yy1absent
Irf1absent
Klf16absent
Wt1absent
Elk3absent
Zfp143absent
Klf5absent
Pbx3absent
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_17-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_17-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_17-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 19, # seqlets: 24651, Positive for: aB_CD40+IL4;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_17-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_17-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_17-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 15, # seqlets: 5944, Negative for: aB_CD40+IL4;A;CL
  • pattern_0: # seqlets: 1225 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Dbx1, Tlx2, Esx1, Lhx5, Otp

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1199 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Glis1, Zbtb7b, Zbtb7a, Zic5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1129 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 733 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr1h2, Ppara, Hnf4g, Nr1h4, Nr2f2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 569 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Snai2, Zeb1, Id4, Mesp2, Scrt2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 178 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxm1, Foxj1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 170 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bach1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 140 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 133 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 133 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 105 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 78 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Rreb1, Zfp281, Zfp148, Klf4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 69 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 38 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 45 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Maz, Rreb1, Zfp281, Sp3, Zfp148

    SequenceContrib ScoresHyp_Contrib Scores