In [1]:
# Parameters
sample_name = "memT;CD4+;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_2-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_2-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 15:12:57,851 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeCD25CCR6 DN CD4 (memory CD4+ T cell)
    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
    rep11219529521410.576255827708123367510.221185876410.1539185873600.3331
    Modelling Metadata
    MetricValue
    auPRC0.5908
    Calibrated Recall at 50% FDR0.211
    Number of Positive Examples in Test Data101831
    Number of Negative Examples in Test Data7969020
    Imbalance Ratio in Test Data0.0126
    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
Pbx3
Irf1
Ctcf
Sp3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Rfx1absent
Runx2absent
9430076C15Rikabsent
Mbtps2absent
Tbpl2absent
Hsf1absent
Tcf7l2absent
Ergabsent
Fosabsent
Klf16absent
Nfiaabsent
Smarcc2absent
Ets1absent
Tcfebabsent
Relaabsent
Unique Homer Motifs
Motif NameModiscoHomer
Mbd2absent
Zfp143absent
Smarcc1absent
Etv1absent
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_2-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_2-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_2-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 25, # seqlets: 24399, Positive for: memT;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_2-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_2-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_2-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 17, # seqlets: 6114, Negative for: memT;CD4+;A;CL
  • pattern_0: # seqlets: 2095 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Glis1, Zbtb7b, Zbtb7a, Zic5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 823 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 749 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rest

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 720 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 245 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 234 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 204 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 171 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 152 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 143 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, E2f1, Zfx, Ctcfl, Tcfap2d

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 129 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 88 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Jund, Batf, Fosb, Fos, Bach1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 83 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 87 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Myc, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 67 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 66 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 58 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores