In [1]:
# Parameters
sample_name = "NCR+ILC3+IL23;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_85-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_85-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 19:24:39,057 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeNCR+ILC3+IL23
    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
    rep11141968259621.33781275566229894410.234723426380.183942624740.3347
    rep21141968259613.86663694660383912680.227253235760.1442121809830.3299
    Modelling Metadata
    MetricValue
    auPRC0.5675
    Calibrated Recall at 50% FDR0.22
    Number of Positive Examples in Test Data98429
    Number of Negative Examples in Test Data7972422
    Imbalance Ratio in Test Data0.0122
    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
Rela
Smarcc2
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Nfe2l2absent
Gata2absent
Bach2absent
Nfiaabsent
Sp3absent
Mef2dabsent
Smarcc1absent
Creb3absent
Foxi1absent
Runx2absent
Rfx1absent
Irf1absent
Mbtps2absent
Ets1absent
Rorcabsent
Ergabsent
Tbpl2absent
Unique Homer Motifs
Motif NameModiscoHomer
Creb1absent
Yy1absent
Pbx3absent
Fosabsent
Klf5absent
Gabpaabsent
Runx1absent
Prdm1absent
Tcfecabsent
Hmga2absent
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_85-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_85-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_85-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 24, # seqlets: 23812, Positive for: NCR+ILC3+IL23;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_85-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_85-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_85-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 18, # seqlets: 6466, Negative for: NCR+ILC3+IL23;A;CL
  • pattern_0: # seqlets: 3341 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1016 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 603 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 370 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 303 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 165 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 83 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Zfx, E2f1, Wt1, Tcfap2d

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 87 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 79 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rreb1, Maz, Egr2, Zfp148, Sp3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 61 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Maz, Rreb1, Zfp148, Sp3, Zfp281

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 50 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Zbtb7a, Wt1, E2f1, Zfx

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 48 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 56 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Myc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 37 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rreb1, Sp3, Maz, Zfp148, Zfp281

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 33 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Sp2, E2f1, Zbtb7a, Zfx

    SequenceContrib ScoresHyp_Contrib Scores