In [1]:
# Parameters
sample_name = "MPP;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_0-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_0-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 15:06:49,319 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeMPP
    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
    rep11277679370613.45283648676687027370.238658459640.1603125804550.345
    rep21277679370610.77893744713532358850.086527548680.0736128905930.3444
    Modelling Metadata
    MetricValue
    auPRC0.6045
    Calibrated Recall at 50% FDR0.215
    Number of Positive Examples in Test Data111476
    Number of Negative Examples in Test Data7959375
    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
Common Motifs
Motif NameModiscoHomer
Sfpi1
Sp3
Irf1
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Nfe2absent
Tcfecabsent
Restabsent
Hoxc9absent
Mbtps2absent
Ergabsent
Rfx1absent
Mef2aabsent
Cebpbabsent
Hsf1absent
Runx2absent
Foxi1absent
Nfiaabsent
Smarcc2absent
Ets1absent
Unique Homer Motifs
Motif NameModiscoHomer
E2f3absent
Wt1absent
Zfp143absent
Creb3absent
Pbx3absent
Yy1absent
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_0-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_0-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_0-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 27, # seqlets: 26308, Positive for: MPP;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_0-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_0-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_0-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 19, # seqlets: 9634, Negative for: MPP;A;CL
  • pattern_0: # seqlets: 2052 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1543 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1360 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis1, Zbtb7b, Zic5, Zic4, Glis2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 960 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Ets1, ENSMUSG00000044690, Elf5, Fev

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 746 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 610 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 603 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 520 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1, Runx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 449 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcf21, Zfp238, Bhlha15, Tcf15, Msc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 127 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf, Ctcfl

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 97 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Nfe2, Jund, Fos, Batf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 110 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Hsf1, Nr6a1, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 86 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 89 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5, Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 87 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 59 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Nr5a2, Nr6a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 56 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 45 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 35 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores