In [1]:
# Parameters
sample_name = "wES;FaceP;E11.5;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_261-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_261-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.
2019-07-23 04:27:47,913 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeembryonic facial prominence(e11.5)
    Cell GroupES cells and embryonic tissues
    Experiment NameDHS
    Experiment GroupENCODE
    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
    rep120487713311411.199106771438209631960.1964124176510.1163444841690.4167
    Modelling Metadata
    MetricValue
    auPRC0.6746
    Calibrated Recall at 50% FDR0.184
    Number of Positive Examples in Test Data110256
    Number of Negative Examples in Test Data7960595
    Imbalance Ratio in Test Data0.0137
    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
Rest
Ctcf
Tcf21
Pbx3
Rfx1
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Creb3absent
Mbtps2absent
Sp2absent
Tcfap2aabsent
Lhx5absent
E2f1absent
Tcfebabsent
Hsf1absent
Nfiaabsent
Smarcc2absent
Rfx8absent
Ergabsent
Sox3absent
Unique Homer Motifs
Motif NameModiscoHomer
E4f1absent
Yy1absent
Sp3absent
Prrx2absent
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_261-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_261-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_261-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 21, # seqlets: 24818, Positive for: wES;FaceP;E11.5;D;En
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_261-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_261-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_261-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 13, # seqlets: 4638, Negative for: wES;FaceP;E11.5;D;En
  • pattern_0: # seqlets: 1957 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 671 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rreb1, Glis3, Zfp281, Zbtb7a, Zfp148

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 636 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfia, Nfix, Nfib, Nfic

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 350 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 267 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 256 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Obox5, Pitx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 107 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Nfe2, Fos, Jund, Batf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 102 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 97 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 48 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 45 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 65 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 37 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rreb1

    SequenceContrib ScoresHyp_Contrib Scores