In [1]:
# Parameters
sample_name = "Spleen;8wks;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_266-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_266-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 04:44:11,320 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typespleen(adult-8wks)
    Cell GroupOther 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
    rep1768355101022.70512060331747624940.231336168080.175774162470.3602
    rep2768355101018.16242501566140628390.162534323060.137388881480.3555
    Modelling Metadata
    MetricValue
    auPRC0.5814
    Calibrated Recall at 50% FDR0.22
    Number of Positive Examples in Test Data65465
    Number of Negative Examples in Test Data8005386
    Imbalance Ratio in Test Data0.0081
    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
Mbtps2
Ctcf
Sp3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Tcfebabsent
Ergabsent
Tbpl2absent
Relbabsent
Foxi1absent
Smarcc2absent
Runx2absent
Hsf1absent
Fosabsent
Atf7absent
Nfibabsent
Rfx1absent
Bcl11aabsent
Sfpi1absent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Creb3absent
Nfkb1absent
Ets1absent
Prdm1absent
Rfx4absent
Sp1absent
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_266-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_266-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_266-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 20, # seqlets: 27854, Positive for: Spleen;8wks;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_266-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_266-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_266-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 22, # seqlets: 5981, Negative for: Spleen;8wks;D;En
  • pattern_0: # seqlets: 2274 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b, Tbp, Ahctf1, Arid3b, Onecut1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1101 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 609 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxp4, Foxn3, Foxj1, Foxm1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 359 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcf15, Zfp238, Tcf21, Msc, Bhlha15

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 217 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 213 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 124 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut1, Onecut3, Onecut2, Cux2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 121 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zkscan1, Zscan4c, Zscan4, Hif3a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 121 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 124 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 101 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 95 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 75 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Nr6a1, Nr5a1, Esrrb, Ppara

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 69 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 59 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Jund, Fos, Fosb, Junb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 51 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zscan4c

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 52 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143, Max

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 41 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 41 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1, Nr5a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 52 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

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

    SequenceContrib ScoresHyp_Contrib Scores