In [1]:
# Parameters
sample_name = "SKLTL_Muscle;8wks;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_265-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_265-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 04:40:48,005 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeskeletal muscle tissue(adult-8wks)
    Cell GroupOther Tissues
    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
    rep1146772909929.667678235884127898240.163575459540.0965321969380.4116
    rep21467729099213.81742408303636726330.152627091300.112697779760.4063
    Modelling Metadata
    MetricValue
    auPRC0.5371
    Calibrated Recall at 50% FDR0.269
    Number of Positive Examples in Test Data98235
    Number of Negative Examples in Test Data7972616
    Imbalance Ratio in Test Data0.0122
    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
Ascl2
Sp2
Mbtps2
Ebf1
Ctcf
Smarcc2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
9430076C15Rikabsent
Nfiaabsent
Rfx1absent
Tcfecabsent
Rfx8absent
Mef2aabsent
Nfe2absent
Hsf1absent
Pbx3absent
Nr3c1absent
Cebpbabsent
Elk1absent
Unique Homer Motifs
Motif NameModiscoHomer
Nficabsent
Elk4absent
Mef2dabsent
Fosabsent
Jdp2absent
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_265-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_265-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_265-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 22, # seqlets: 21065, Positive for: SKLTL_Muscle;8wks;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_265-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_265-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_265-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 24, # seqlets: 8901, Negative for: SKLTL_Muscle;8wks;D;En
  • pattern_0: # seqlets: 2252 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Mesp2, Id4, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1339 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 969 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7c, Gli3, Gli1, Gli2, Hic2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 929 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7a, Zbtb7b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 880 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 619 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfic, Nfix, Nfia, Nfib, Hic1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 314 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 172 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 164 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Spib, Sfpi1, Spic, Bcl11a, Etv6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 157 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcf15, Tal1, Msc, Tcf21, Zfp238

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 151 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 136 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Klf1, Klf4, Klf8, Klf2, Klf12

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 135 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Nfe2, Smarcc1, Bach1, Fosb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 97 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 91 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 88 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 68 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr6a1, Esrrb, Nr5a2, Esrrg, Nr5a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 48 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 48 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Myc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 82 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143, Smarcc2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 42 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 30 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf

    SequenceContrib ScoresHyp_Contrib Scores