In [1]:
# Parameters
sample_name = "NPC;Ch13;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_172-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_172-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 23:58:01,672 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeneural progenitor cells(Ch13)
    Cell GroupNeural Cells and Tissues
    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
    rep119031812497310.354786662422141292440.163167417210.0778311470190.3595
    Modelling Metadata
    MetricValue
    auPRC0.6109
    Calibrated Recall at 50% FDR0.305
    Number of Positive Examples in Test Data111190
    Number of Negative Examples in Test Data7959661
    Imbalance Ratio in Test Data0.0138
    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
Rfx1
Nfia
Pbx3
Creb3
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Zeb1absent
Mef2cabsent
Erfabsent
Smarcc2absent
Sox3absent
Restabsent
Myogabsent
Fosabsent
Tbpl2absent
Sp3absent
Unique Homer Motifs
Motif NameModiscoHomer
Klf5absent
Zfp143absent
Gabpaabsent
Sox17absent
Ascl2absent
Tcfebabsent
Mafaabsent
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_172-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_172-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_172-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 22, # seqlets: 19619, Positive for: NPC;Ch13;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_172-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_172-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_172-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 22, # seqlets: 11749, Negative for: NPC;Ch13;A;GEO
  • pattern_0: # seqlets: 2998 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b, Cux2, Dbx1, Pit1, Pou4f3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2100 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1385 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox9, Sox17, Sox6, Sox2, Sox14

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1161 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rfx2, Rfx1, Rest

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 900 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Nr2f6, Rarb, Rxra, Nr1h2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 683 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ascl2, Tcf21, Msc, Atoh1, Tcf3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 421 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 348 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 216 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 201 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 180 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Ets1, Etv5, Elk3, Etv6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 164 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfic

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 172 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 155 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 140 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Maz, Sp2, E2f1, Zfp148

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 103 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 89 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 89 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 82 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 79 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 47 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 36 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores