In [1]:
# Parameters
sample_name = "naiveT;CD8+;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_113-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_113-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 20:54:38,447 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeNaive CD8+ T cell
    Cell GroupT cells
    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
    rep115188812933812.24762344040170817390.302351774820.22185578840.3654
    rep215188812933812.46231794372841302090.230433833270.188761242260.3416
    rep315188812933813.73141878080464542480.34445890650.244669484710.3703
    Modelling Metadata
    MetricValue
    auPRC0.5965
    Calibrated Recall at 50% FDR0.201
    Number of Positive Examples in Test Data123800
    Number of Negative Examples in Test Data7947051
    Imbalance Ratio in Test Data0.0153
    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
Sp3
Ctcf
Smarcc2
Tcfeb
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Rfx8absent
Runx1absent
Creb3absent
Relaabsent
Sp2absent
Ets1absent
Fosabsent
Hsf1absent
Mbtps2absent
Nfiaabsent
Foxi1absent
Rfx2absent
Irf1absent
Unique Homer Motifs
Motif NameModiscoHomer
E4f1absent
Tcfap2dabsent
Erfabsent
Pbx3absent
Irf3absent
Yy1absent
Runx2absent
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_113-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_113-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_113-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 25, # seqlets: 23482, Positive for: naiveT;CD8+;A;GEO
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_113-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_113-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_113-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 21, # seqlets: 11486, Negative for: naiveT;CD8+;A;GEO
  • pattern_0: # seqlets: 1974 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1680 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1675 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b, Arid3b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1429 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Maz, Rreb1, Zfp148, Zfp281

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 1218 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Zbtb7a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 1018 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sebox, Dbx1, Tlx2, Pou4f3, Esx1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 750 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7c, Gli1, Gli3, Gli2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 331 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hoxb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 296 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 203 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 151 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp238, Tcf15, Bhlha15, Tcf21, Neurog1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 145 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 102 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 100 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 93 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 80 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 59 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 56 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    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: 40 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 38 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores