In [1]:
# Parameters
sample_name = "WHL_BRN;8wks;D;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_212-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_212-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 02:05:18,978 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeWhole Brain (adult-8wks)
    Cell GroupNeural Cells and Tissues
    Experiment NameDHS
    Experiment GroupGEO
    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
    rep126063517369910.6646118439720360433520.3043137681660.1163595955620.5032
    Modelling Metadata
    MetricValue
    auPRC0.5919
    Calibrated Recall at 50% FDR0.247
    Number of Positive Examples in Test Data164846
    Number of Negative Examples in Test Data7906005
    Imbalance Ratio in Test Data0.0204
    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
Sp2
Fos
Tal1
Ctcf
Dbp
Nfic
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Smarcc2absent
Rfx1absent
Mbtps2absent
Mef2aabsent
Egr2absent
Rorcabsent
9430076C15Rikabsent
Sox3absent
Erfabsent
Pbx3absent
Rfx8absent
Bach2absent
Nfiaabsent
Ascl2absent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Rfx2absent
Nfkb1absent
Sp8absent
E4f1absent
Mef2cabsent
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_212-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_212-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_212-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 21, # seqlets: 24027, Positive for: WHL_BRN;8wks;D;GEO
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_212-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_212-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_212-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 19, # seqlets: 11016, Negative for: WHL_BRN;8wks;D;GEO
  • pattern_0: # seqlets: 2407 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2126 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Cux2, Hmg20b, Pou4f3, Arid3b, Dbx1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1868 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1035 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp1, Klf6, Klf16, Sp4, Plagl1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 663 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp238, Tcf4, Bhlha15, Tcf21, Twist2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 560 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7c, Gli3, Gli1, Gli2, Hic2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 542 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 495 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox17, Sox6, Sox9

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 331 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 248 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2, Nfe2l2, Jund, Fos, Smarcc1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 141 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 131 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Sfpi1, Spib

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 79 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Sfpi1, Spib, Irf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 77 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 72 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Sfpi1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 56 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 76 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

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

    Bcl6, Sfpi1, Spib, Irf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 69 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1

    SequenceContrib ScoresHyp_Contrib Scores