In [1]:
# Parameters
sample_name = "Tfh_mut;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_25-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_25-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 16:22:34,946 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeTfh (CD4+CD44+CXCR5+PD1+CD25-) Mut
    Cell GroupT 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
    rep11109858732411.874754846739114899300.209682371260.1502179319200.3271
    Modelling Metadata
    MetricValue
    auPRC0.607
    Calibrated Recall at 50% FDR0.214
    Number of Positive Examples in Test Data98428
    Number of Negative Examples in Test Data7972423
    Imbalance Ratio in Test Data0.0122
    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
Smarcc2
Ctcf
Irf1
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Ets1absent
Fevabsent
Jundabsent
Sp3absent
Unique Homer Motifs
Motif NameModiscoHomer
Sp2absent
Yy1absent
Erfabsent
E2f1absent
Nfkb1absent
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_25-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_25-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_25-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 8, # seqlets: 13397, Positive for: Tfh_mut;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_25-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_25-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_25-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 14, # seqlets: 5138, Negative for: Tfh_mut;A;CL
  • pattern_0: # seqlets: 1931 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Glis1, Zbtb7b, Zbtb7a, Zic5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1192 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tbp, Hmg20b, Arid3b, Onecut1, Ahctf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 966 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Tcf4, Mga, Tcf3, Mesp2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 223 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 175 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1, Runx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 155 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 89 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 75 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 71 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 67 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 57 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 68 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 38 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 31 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores