In [1]:
# Parameters
sample_name = "restingB;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_73-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_73-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 18:48:11,456 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typerestingB
    Cell GroupB 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
    rep1451293111713.02535448049944149930.081147425840.0871172184150.3162
    Modelling Metadata
    MetricValue
    auPRC0.7228
    Calibrated Recall at 50% FDR0.16
    Number of Positive Examples in Test Data39260
    Number of Negative Examples in Test Data8031591
    Imbalance Ratio in Test Data0.0049
    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
Jdp2
Pbx3
Ctcf
Bcl11a
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Tbpl2absent
Relbabsent
Mef2aabsent
Nfiaabsent
Tcfecabsent
Smarcc2absent
Ets1absent
Rfx1absent
Hsf1absent
Sp3absent
Mbtps2absent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Klf5absent
E4f1absent
Elk3absent
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_73-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_73-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_73-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 18, # seqlets: 23337, Positive for: restingB;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_73-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_73-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_73-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 20, # seqlets: 7606, Negative for: restingB;A;CL
  • pattern_0: # seqlets: 1768 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Glis2, Zbtb7a, Glis1, Zic5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1124 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcf15, Olig1, Tcf21, Msc, Olig2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 907 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Scrt2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 761 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 627 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 536 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7c, Gli3, Gli1, Gli2, Hic2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 415 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 316 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 261 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 131 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Mef2a, Mef2c, Mef2d, Mef2b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 125 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 115 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tbpl2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 92 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) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 66 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 64 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 62 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Spib, Etv6, Erf, Etv5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 59 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rreb1, Zfp281, Zfp148

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 42 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Elf4, Elf3, Elf2, Etv6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 48 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3

    SequenceContrib ScoresHyp_Contrib Scores