In [1]:
# Parameters
sample_name = "preB;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_6-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_6-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 15:24:26,999 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typepreB cells
    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
    rep1969157493810.40914978707272631090.145955659820.1118162316260.3261
    Modelling Metadata
    MetricValue
    auPRC0.6153
    Calibrated Recall at 50% FDR0.209
    Number of Positive Examples in Test Data81027
    Number of Negative Examples in Test Data7989824
    Imbalance Ratio in Test Data0.01
    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
Common Motifs
Motif NameModiscoHomer
Pbx3
Ctcf
Sp3
Sfpi1
Ebf1
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Mef2dabsent
Ascl2absent
Klf16absent
Tbpl2absent
Nfiaabsent
Pax5absent
Smarcc2absent
Bcl11aabsent
Sp2absent
Tcfebabsent
Jdp2absent
Rfx1absent
Mbtps2absent
Runx1absent
Pax1absent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp161absent
Zfp143absent
E4f1absent
Ferd3labsent
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_6-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_6-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_6-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 23, # seqlets: 24262, Positive for: preB;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_6-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_6-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_6-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 20, # seqlets: 6623, Negative for: preB;A;CL
  • pattern_0: # seqlets: 2101 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1871 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Dbx1, Tlx2, Arid3b, Sebox, Pou4f1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 489 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 276 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gli1, Gli3, Gli2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 224 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcf15, Tal1, Bhlha15, Tcf4, Tcf21

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 212 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 196 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 176 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1, Foxn3, Foxp4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 173 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 162 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

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

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 95 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

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

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

    Nr5a2, Esrrb, Nr6a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 67 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Maz, Sfpi1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 65 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1, Nr5a1, Prdm4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 59 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 50 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 47 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores