In [1]:
# Parameters
sample_name = "SPNL_CHRD;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_62-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_62-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 18:14:13,884 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typespinal cord
    Cell GroupNeural Cells and Tissues
    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
    rep149343277017.60515096140421875850.042934141410.067168575420.3309
    Modelling Metadata
    MetricValue
    auPRC0.692
    Calibrated Recall at 50% FDR0.199
    Number of Positive Examples in Test Data33076
    Number of Negative Examples in Test Data8037775
    Imbalance Ratio in Test Data0.0041
    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
Mbtps2
Gabpa
Ctcf
Sp3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Tcfebabsent
Smarcc2absent
Sox6absent
Creb3absent
Rfx2absent
Tbpl2absent
Irf1absent
Nfiaabsent
Rfx8absent
Foxi1absent
E2f1absent
Sp2absent
Unique Homer Motifs
Motif NameModiscoHomer
E4f1absent
Pbx3absent
Ctcflabsent
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_62-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_62-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_62-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 24, # seqlets: 20496, Positive for: SPNL_CHRD;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_62-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_62-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_62-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 33, # seqlets: 9163, Negative for: SPNL_CHRD;A;CL
  • pattern_0: # seqlets: 1551 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Scrt1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1390 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1099 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tbp, Phf21a, Ahctf1, Hmg20b, Onecut1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 467 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Msc, Tcf21, Neurog1, Neurod2, Olig2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 452 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 423 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 422 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Rarb, Rxra, Rara, Nr2f6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 310 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b, Hmg20b, Dbx1, Phf21a, Pit1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 273 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 235 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Nr6a1, Esrrb, Hnf4g

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 236 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 226 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 222 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b, Dbx1, Pit1, Phf21a, Pou4f3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 166 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 154 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 152 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b, Dbx1, Tlx2, Lhx3, Lhx5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 142 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata4, Gata1, Gata2, Gata6, Gata3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 139 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 131 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox6, Sox17, Sox9, Sox2, Sox3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 134 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 112 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 107 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hif3a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 85 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 80 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_24: # seqlets: 69 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_25: # seqlets: 60 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_26: # seqlets: 57 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_27: # seqlets: 57 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Klf1, Klf4, Klf2, Klf8, Klf12

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_28: # seqlets: 52 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_29: # seqlets: 43 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_30: # seqlets: 43 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_31: # seqlets: 37 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_32: # seqlets: 37 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores