In [1]:
# Parameters
sample_name = "ILC2_Nippo;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_83-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_83-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 19:19:12,131 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeILC2 (Nippo infected)
    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
    rep11230169564310.9951626771115617800.22471932970.1394175194860.3395
    Modelling Metadata
    MetricValue
    auPRC0.5752
    Calibrated Recall at 50% FDR0.226
    Number of Positive Examples in Test Data113094
    Number of Negative Examples in Test Data7957757
    Imbalance Ratio in Test Data0.014
    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
Irf1
Fos
Nfkb1
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Nfixabsent
Mbtps2absent
Ergabsent
Klf16absent
Foxi1absent
Runx2absent
Tcfap2dabsent
Smarcc2absent
9430076C15Rikabsent
Bach2absent
Sp3absent
Ets1absent
Rorcabsent
Rfx1absent
Gata2absent
Unique Homer Motifs
Motif NameModiscoHomer
Erfabsent
Sp2absent
Pbx3absent
Zfp143absent
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_83-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_83-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_83-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 21, # seqlets: 22891, Positive for: ILC2_Nippo;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_83-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_83-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_83-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 19, # seqlets: 7948, Negative for: ILC2_Nippo;A;CL
  • pattern_0: # seqlets: 1378 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 950 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Glis1, Zbtb7a, Zbtb7b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 832 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Nr4a1, Esrrb, Nr4a3, Esrrg

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 820 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata6, Gata5, Gata3, Gata2, Gata4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 719 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ets1, Erg, Etv5, Etv6, Fli1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 622 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rfx2, Rfx1, Arid2, Rest

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 619 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 420 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Nfe2, Fos, Jund, Smarcc1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 388 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Maz, Zfp281, Zfp148, Rreb1, Sp3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 216 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gli1, Gli3, Gli2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 215 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 175 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 145 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 138 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Egr2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 100 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 67 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 63 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 40 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

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

    Nr5a2, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores