In [1]:
# Parameters
sample_name = "preB_BMD;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_140-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_140-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 22:11:30,838 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeBone marrow derived pre-B cell
    Cell GroupB cells
    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
    rep115779812902618.843330832398104480810.339160836090.1974116548670.3782
    rep215779812902618.664930807421107137790.34862469980.2029118673940.3855
    Modelling Metadata
    MetricValue
    auPRC0.6207
    Calibrated Recall at 50% FDR0.209
    Number of Positive Examples in Test Data139188
    Number of Negative Examples in Test Data7931663
    Imbalance Ratio in Test Data0.0172
    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
Sfpi1
Ctcf
Ascl2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Mef2aabsent
Pax5absent
Sp3absent
Bcl11aabsent
Mbtps2absent
Foxi1absent
Tcfecabsent
Creb3absent
Tbpl2absent
Elk3absent
Smarcc2absent
Rfx1absent
Nfiaabsent
Runx1absent
Ebf1absent
Unique Homer Motifs
Motif NameModiscoHomer
Rfx7absent
Zfp161absent
Pbx3absent
Pax9absent
Sp2absent
Tbx2absent
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_140-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_140-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_140-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 21, # seqlets: 25627, Positive for: preB_BMD;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_140-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_140-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_140-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 15, # seqlets: 9051, Negative for: preB_BMD;A;GEO
  • pattern_0: # seqlets: 2556 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Stat5b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2464 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Atoh8

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 2001 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rxrg, Rxrb, Glis1, Nr2f1, Glis2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 536 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1, Foxn3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 372 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 206 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 202 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 158 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Maz, Zfp148, Zfp281, Rreb1, Sp3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 140 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 91 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Maz, Sp3, Zfp148, Zfp281, Rreb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 78 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 69 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Maz, Sp3, Zfp281, Bcl6, Zfp148

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 64 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 59 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 55 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores