In [1]:
# Parameters
sample_name = "LNG_TRM_HSC;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_75-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_75-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 18:54:25,681 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeLong Term HSC
    Cell GroupOther Immune Cells
    Experiment NameATAC
    Experiment GroupCasellas Lab
    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
    rep1113997779737.34763318040630654470.092438974580.1175115296210.3477
    rep21139977797324.57931329310844956360.338736427410.274450580720.3811
    Modelling Metadata
    MetricValue
    auPRC0.6176
    Calibrated Recall at 50% FDR0.195
    Number of Positive Examples in Test Data90532
    Number of Negative Examples in Test Data7980319
    Imbalance Ratio in Test Data0.0112
    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
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Irf1absent
Nfiaabsent
Hsf1absent
Klf16absent
Mef2babsent
Jdp2absent
Sp3absent
Restabsent
Runx2absent
Smarcc2absent
Rfx1absent
Foxi1absent
Nfe2l2absent
Tbpl2absent
Tcfecabsent
Hoxc9absent
Mbtps2absent
Ets1absent
Gata6absent
Unique Homer Motifs
Motif NameModiscoHomer
Elk3absent
Yy1absent
Prdm1absent
E2f1absent
Zfp143absent
Gata2absent
Pbx3absent
Sp2absent
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_75-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_75-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_75-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 23, # seqlets: 23184, Positive for: LNG_TRM_HSC;A;CL
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_75-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_75-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_75-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 22, # seqlets: 8208, Negative for: LNG_TRM_HSC;A;CL
  • pattern_0: # seqlets: 2134 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Rarb, Esrrg, Nr2f6, Nr4a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1584 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1235 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 627 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata6, Gata2, Gata5, Gata4, Gata3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 391 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 365 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1, Runx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 351 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 270 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 201 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 155 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 130 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hif3a, Egr2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 98 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rreb1, Vdr

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 97 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Egr2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 87 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 92 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 74 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 68 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 67 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hoxb1, Pbx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 59 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 54 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 35 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 34 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcfap2c, Sp3, Klf6, Egr1, Wt1

    SequenceContrib ScoresHyp_Contrib Scores