In [1]:
# Parameters
sample_name = "iPV_NRN;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_175-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_175-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.
2019-07-23 00:08:27,397 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeparvalbumin-positive (PV) inhibitory neurons
    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
    rep12444151754638.2016107232529182942590.1706100752270.094403503390.3764
    rep22444151754639.430789739894164896260.183889373260.0996338357290.3771
    Modelling Metadata
    MetricValue
    auPRC0.5743
    Calibrated Recall at 50% FDR0.255
    Number of Positive Examples in Test Data177059
    Number of Negative Examples in Test Data7893792
    Imbalance Ratio in Test Data0.0219
    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
Pbx3
Ctcf
Fos
Dbp
Rfx1
Rorc
Gabpa
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Bach1absent
Nfiaabsent
Tcf12absent
9430076C15Rikabsent
Wt1absent
Mbtps2absent
Zfp281absent
Tcfebabsent
Sp3absent
Mef2aabsent
Smarcc2absent
Phox2babsent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Meox2absent
Mef2cabsent
Mazabsent
Myogabsent
Klf5absent
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_175-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_175-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_175-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 20, # seqlets: 20015, Positive for: iPV_NRN;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_175-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_175-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_175-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 23, # seqlets: 14170, Negative for: iPV_NRN;A;GEO
  • pattern_0: # seqlets: 2792 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rxrg, Rxrb, Glis2, Nr2f1, Nr2f2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2199 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut1, Arid3b, Onecut3, Pou4f3, Pit1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 2195 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1107 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox9, Sox17, Sox6, Sox2, Sox14

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 996 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 871 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 680 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut3, Onecut1, Onecut2, Hmg20b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 472 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Klf1, Klf3, Klf2, Klf4, Klf8

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 426 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 419 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 415 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 395 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 243 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 148 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 147 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata2, Gata6, Gata1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 147 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcf3, Tcfap4, Atoh1, Ascl2, Tcf12

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 114 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Smarcc1, Fos, Bach1, Fosb, Nfe2l2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 94 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Pitx2, AC189028.1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 87 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Mef2a, Mef2c, Mef2b, Mef2d

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 87 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf, Ctcfl

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 64 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 38 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 34 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Spib, Sfpi1

    SequenceContrib ScoresHyp_Contrib Scores