In [1]:
# Parameters
sample_name = "DP;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_46-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_46-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 17:25:09,812 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeDP
    Cell GroupT 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
    rep113052310745613.180951321601122433110.238775572850.1473175510610.3421
    Modelling Metadata
    MetricValue
    auPRC0.583
    Calibrated Recall at 50% FDR0.217
    Number of Positive Examples in Test Data109973
    Number of Negative Examples in Test Data7960878
    Imbalance Ratio in Test Data0.0136
    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
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Id4absent
Rfx2absent
Rfx8absent
Creb3absent
Tcfebabsent
Rorcabsent
Sp3absent
Mbtps2absent
Foxi1absent
Runx2absent
Nfibabsent
Mef2dabsent
Irf1absent
Smarcc2absent
Ets1absent
Sp2absent
Bach1absent
Gabpaabsent
Unique Homer Motifs
Motif NameModiscoHomer
Pbx3absent
Klf5absent
Mesp2absent
Yy1absent
Etv1absent
Zfp143absent
Zfp281absent
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_46-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_46-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_46-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 22, # seqlets: 23696, Positive for: DP;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_46-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_46-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_46-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 24, # seqlets: 7249, Negative for: DP;A;CL
  • pattern_0: # seqlets: 1572 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1026 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 731 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 565 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Glis1, Zbtb7b, Zic5, Glis3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 516 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx2, Runx1, Runx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 448 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 335 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rfx2, Rfx1, Rest

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 291 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 235 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Nr5a2, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 198 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Jund, Nfe2, Batf, Fosb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 191 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 177 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 167 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 127 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 96 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Klf15, Maz, Sp2, Zfp148

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

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 74 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

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

    Zscan4, Zkscan1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 83 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 70 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1, Nr5a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 55 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 53 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 39 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 37 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores