In [1]:
# Parameters
sample_name = "ES;ZhBTc4;1;D;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_198-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_198-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 01:26:34,737 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeUndifferentiated mouse embryonic stem cells (ZhBTc4)
    Cell GroupES cells and embryonic tissues
    Experiment NameDHS
    Experiment GroupGEO
    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
    rep12218811622769.5562111711203287649730.2575142584100.1277458338450.4104
    Modelling Metadata
    MetricValue
    auPRC0.6826
    Calibrated Recall at 50% FDR0.168
    Number of Positive Examples in Test Data133495
    Number of Negative Examples in Test Data7937356
    Imbalance Ratio in Test Data0.0165
    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
Pbx3
Ctcf
Tcfec
Rest
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Sp3absent
Trp63absent
Nr5a2absent
Hsf1absent
Klf14absent
Gabpaabsent
Nfibabsent
Tcfcp2l1absent
Sox17absent
Tcfap2aabsent
Mbtps2absent
Nfe2l2absent
Creb3absent
Tbpl2absent
Smarcc2absent
Rfx1absent
Unique Homer Motifs
Motif NameModiscoHomer
Nr5a1absent
Etv5absent
Tcfap2babsent
Sox9absent
Nfe2absent
Klf5absent
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_198-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_198-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_198-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 26, # seqlets: 22814, Positive for: ES;ZhBTc4;1;D;GEO
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_198-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_198-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_198-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 16, # seqlets: 10415, Negative for: ES;ZhBTc4;1;D;GEO
  • pattern_0: # seqlets: 4051 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b, Pit1, Phf21a, Onecut1, Onecut3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2443 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Zbtb7b, Zbtb7a, Zic5, Plagl1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1389 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hic1, Hic2, Nfic

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 495 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 461 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 383 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 190 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 177 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 155 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox9, Sox17, Sox6, Sox2, Sox14

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 140 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 130 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 140 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 82 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) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 51 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 51 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores