In [1]:
# Parameters
sample_name = "prePLSM_B;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_138-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_138-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 22:05:55,371 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typePre-PB
    Cell GroupB cells
    Experiment NameATAC
    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
    rep114368411056917.341432240553100788460.312866287720.2057119977540.3723
    rep214368411056914.95335166312100085830.284860710450.1727143190070.4074
    Modelling Metadata
    MetricValue
    auPRC0.5913
    Calibrated Recall at 50% FDR0.198
    Number of Positive Examples in Test Data120867
    Number of Negative Examples in Test Data7949984
    Imbalance Ratio in Test Data0.015
    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
Ctcf
Ebf1
Mbtps2
Pbx3
Smarcc2
Sfpi1
Tbpl2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Relaabsent
Mef2dabsent
Creb3absent
Batfabsent
Sp3absent
Irf1absent
Tcfebabsent
Hsf1absent
Rfx1absent
E2f1absent
Ascl2absent
Unique Homer Motifs
Motif NameModiscoHomer
Tcf3absent
E4f1absent
Mafaabsent
Sp2absent
Stat2absent
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_138-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_138-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_138-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 22, # seqlets: 26578, Positive for: prePLSM_B;A;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_138-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_138-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_138-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 19, # seqlets: 9655, Negative for: prePLSM_B;A;GEO
  • pattern_0: # seqlets: 1657 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Scrt2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1562 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Dbx1, Lhx5, Tlx2, Lmx1b, Pou4f1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1458 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Glis1, Glis2, Zbtb7a, Zic5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1377 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 1302 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 454 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 337 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1, Foxp4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 220 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 174 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Ets1, Sfpi1, Bcl11a, Etv6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 164 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 159 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Fos, Nfe2l2, Smarcc1, Nfe2, Batf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 158 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 157 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 132 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tbpl2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 90 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 105 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 51 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 49 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 49 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores