In [1]:
# Parameters
sample_name = "apTreg;D;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_209-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_209-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 01:59:12,817 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeActivated primary T regulatory cells, isolated ex vivo
    Cell GroupT cells
    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
    rep11381821162155.9779143353004331809250.2315185305610.1293531620030.3709
    Modelling Metadata
    MetricValue
    auPRC0.6033
    Calibrated Recall at 50% FDR0.212
    Number of Positive Examples in Test Data103253
    Number of Negative Examples in Test Data7967598
    Imbalance Ratio in Test Data0.0128
    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
Batfabsent
Restabsent
Tbx2absent
Ets1absent
Irf1absent
Ergabsent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Sp2absent
Erfabsent
Irf3absent
Pbx3absent
Tcfcp2absent
Yy1absent
Relaabsent
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_209-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_209-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_209-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 8, # seqlets: 17166, Positive for: apTreg;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_209-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_209-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_209-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 13, # seqlets: 6970, Negative for: apTreg;D;GEO
  • pattern_0: # seqlets: 2482 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2129 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b, Dbx1, Phf21a, Tbp, Ahctf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 840 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 447 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 404 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 228 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 94 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Fosb, Fos, Smarcc1, Jund, Nfe2l2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 94 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Maz, Sfpi1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 61 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 57 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 51 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 52 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Maz, Sfpi1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 31 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Sfpi1, Maz, Bcl11a, Spib

    SequenceContrib ScoresHyp_Contrib Scores