In [1]:
# Parameters
sample_name = "ES;ZhBTc4;2;D;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_199-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_199-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 01:29:40,688 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeUndifferentiated mouse embryonic stem cells (ZhBTc4)
    Cell GroupES cells and embryonic 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
    rep122699916273011.182897964123278338640.2842125486260.1281420210880.429
    Modelling Metadata
    MetricValue
    auPRC0.6699
    Calibrated Recall at 50% FDR0.186
    Number of Positive Examples in Test Data142314
    Number of Negative Examples in Test Data7928537
    Imbalance Ratio in Test Data0.0176
    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
Foxi1
Sox2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Rfx1absent
Gabpaabsent
Sox9absent
E2f1absent
Tcfecabsent
Klf5absent
Restabsent
Tcfap2eabsent
Zic4absent
Bach1absent
Creb3absent
Tcfcp2l1absent
Mbtps2absent
Zfxabsent
Hsf1absent
Smarcc2absent
Esrrbabsent
Unique Homer Motifs
Motif NameModiscoHomer
Nr5a1absent
Klf8absent
Sox6absent
Tcfebabsent
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_199-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_199-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_199-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 24, # seqlets: 24921, Positive for: ES;ZhBTc4;2;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_199-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_199-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_199-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 22, # seqlets: 13303, Negative for: ES;ZhBTc4;2;D;GEO
  • pattern_0: # seqlets: 2319 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut3, Onecut1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2230 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 2116 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 2051 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hic2, Hic1, Nfic

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 1356 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 573 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 490 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Klf1, Klf3, Klf2, Klf4, Klf8

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 454 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox17, Sox9, Sox6, Sox2, Sox14

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 359 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 165 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sfpi1, Etv6, Ets1, Fli1, Elf4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 158 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 156 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox2, Pou5f1, Sox30

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 149 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pou5f1, Sox2, Tbpl2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 142 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143, Myc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 106 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Sfpi1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 104 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Spib, Sfpi1, Spic, Bcl11a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 98 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 63 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 61 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 58 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Sfpi1, Irf1, Maz, Bcl11a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 52 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 43 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores