In [1]:
# Parameters
sample_name = "Th17;CD4+;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_3-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_3-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 15:16:15,303 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeTh17 CD4
    Cell GroupT 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
    rep11174658604210.652652508136102271070.194875283510.1434179931990.3428
    Modelling Metadata
    MetricValue
    auPRC0.6069
    Calibrated Recall at 50% FDR0.22
    Number of Positive Examples in Test Data97092
    Number of Negative Examples in Test Data7973759
    Imbalance Ratio in Test Data0.012
    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
Ets1
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Mbtps2absent
Runx2absent
Irf1absent
Tbpl2absent
Fosabsent
Foxi1absent
Rfx1absent
Ergabsent
Relaabsent
Tcfebabsent
Nfiaabsent
Rfx8absent
9430076C15Rikabsent
Smarcc2absent
Sp3absent
Unique Homer Motifs
Motif NameModiscoHomer
Sp2absent
Zfp161absent
E4f1absent
Smarcc1absent
Pbx3absent
Yy1absent
Nfkb1absent
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_3-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_3-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_3-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 20, # seqlets: 25024, Positive for: Th17;CD4+;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_3-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_3-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_3-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 18, # seqlets: 10587, Negative for: Th17;CD4+;A;CL
  • pattern_0: # seqlets: 2706 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1992 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1380 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 893 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 654 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b, Tbp, Hmg20b, Phf21a, Ahctf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 655 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Rarb, Rxra, Nr2f6, Rara

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 620 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 284 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 282 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hif3a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 243 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637, Arid3b, Hmg20b, Tbp, Onecut1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 240 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 185 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 110 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata4, Gata2, Gata1, Mecom, Gata6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 103 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 75 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 78 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Myc, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 50 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 37 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b

    SequenceContrib ScoresHyp_Contrib Scores