In [1]:
# Parameters
sample_name = "wES;Telenchephalon;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_255-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_255-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 04:09:44,553 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typetelencephalon tissue
    Cell GroupES cells and embryonic tissues
    Experiment NameDHS
    Experiment GroupENCODE
    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
    rep124265114895513.03113805773381630160.214541702120.1096172290320.4528
    rep224265114895513.51462322649241101080.17723407250.1008105936790.4562
    rep324265114895514.2232448053643923140.179525972310.1061110108170.4499
    Modelling Metadata
    MetricValue
    auPRC0.6109
    Calibrated Recall at 50% FDR0.237
    Number of Positive Examples in Test Data191380
    Number of Negative Examples in Test Data7879471
    Imbalance Ratio in Test Data0.0237
    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
Mbtps2
Ctcf
Egr2
Fos
Mef2c
Dbp
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Tcfebabsent
Sox6absent
Rfx8absent
Nfiaabsent
Sp2absent
Erfabsent
Hsf1absent
Rfx1absent
Smarcc2absent
Creb3absent
Tal1absent
Unique Homer Motifs
Motif NameModiscoHomer
E2f1absent
Neurod2absent
Zfp143absent
Gabpaabsent
Rfx2absent
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_255-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_255-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_255-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 19, # seqlets: 27001, Positive for: wES;Telenchephalon;D;En
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_255-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_255-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_255-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 22, # seqlets: 14602, Negative for: wES;Telenchephalon;D;En
  • pattern_0: # seqlets: 3728 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rarb, Rxra, Rara, Ppara, Nr2f2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2581 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Phf21a, Onecut3, Pit1, Pou4f3, Onecut1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1992 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Snai2, Zeb1, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1722 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp238, Tcf15, Tcf21, Bhlha15, Msc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 824 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 712 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 565 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sfpi1, Bcl11a, Spib, Spic, Ets1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 427 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 342 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Smarcc1, Nfe2, Jund, Batf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 303 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Egr2, Zfp740, Sp5, Zfp281, Gli2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 215 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Nr6a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 171 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfic

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 160 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 143 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 133 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 127 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 99 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Mef2a, Mef2c, Mef2b, Mef2d

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 93 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 84 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    AC189028.1, Pitx2, Nr5a2, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 66 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 61 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 54 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores