In [1]:
# Parameters
sample_name = "NIH3T3_FBROBLST;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_219-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_219-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 02:22:06,813 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeFibroblast/NIH3T3
    Cell GroupCancer or Immortalized cells
    Experiment NameDHS
    Experiment GroupENCODE
    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
    rep11818641274939.0817137526751293972050.2138139863150.1017569598880.4142
    rep218186412749316.21212038579746149210.226622879520.112391207500.4478
    Modelling Metadata
    MetricValue
    auPRC0.5662
    Calibrated Recall at 50% FDR0.236
    Number of Positive Examples in Test Data127320
    Number of Negative Examples in Test Data7943531
    Imbalance Ratio in Test Data0.0158
    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
Rest
Mbtps2
Ctcf
Smarcc2
Fos
Nfic
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Mef2aabsent
Foxi1absent
Tcfecabsent
Creb3absent
Hoxa9absent
Runx1absent
Rfx1absent
Ets1absent
Tcf21absent
Sp3absent
Cebpbabsent
Hsf1absent
Nfixabsent
Unique Homer Motifs
Motif NameModiscoHomer
Nfiaabsent
Gabpaabsent
Cebpdabsent
Sp2absent
Zfp238absent
Pbx3absent
Thrbabsent
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_219-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_219-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_219-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 23, # seqlets: 22177, Positive for: NIH3T3_FBROBLST;D;En
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_219-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_219-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_219-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 20, # seqlets: 7012, Negative for: NIH3T3_FBROBLST;D;En
  • pattern_0: # seqlets: 1883 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 860 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rest

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 720 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 685 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Fos, Nfe2l2, Batf, Nfe2, Smarcc1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 600 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 508 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfic

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 305 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bhlha15, Neurog1, Msc, Tcf21, Neurod2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 213 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 195 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Cebpb, Cebpg, Cebpd, Cebpa, Cebpe

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 176 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Cebpb, Cebpa, Jdp2, Creb1, Atf2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 141 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Nr5a2, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 131 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 125 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 106 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 92 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 70 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

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

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 66 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 41 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Cux2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 36 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores