In [1]:
# Parameters
sample_name = "Md_BRN;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_252-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_252-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 04:02:01,236 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typemidbrain(P0)
    Cell GroupNeural Cells and 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
    rep123047814106910.1658128539086221789830.1726NANA539363970.4197
    rep22304781410699.02227919972671979220.090956099400.0708260427120.3289
    Modelling Metadata
    MetricValue
    auPRC0.6323
    Calibrated Recall at 50% FDR0.208
    Number of Positive Examples in Test Data125309
    Number of Negative Examples in Test Data7945542
    Imbalance Ratio in Test Data0.0155
    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
Pax6
Creb3
Nfia
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Wt1absent
Rfx1absent
Rfx8absent
Pbx3absent
Atoh1absent
Mef2dabsent
Erfabsent
Sox3absent
Ebf1absent
Hsf1absent
Mbtps2absent
Smarcc2absent
Sp3absent
Tcfecabsent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Rfx2absent
Neurod1absent
Gabpaabsent
Nficabsent
Zfp637absent
Sp2absent
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_252-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_252-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_252-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 21, # seqlets: 19141, Positive for: Md_BRN;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_252-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_252-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_252-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 12, # seqlets: 7369, Negative for: Md_BRN;D;En
  • pattern_0: # seqlets: 2162 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Snai2, Zeb1, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1399 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rxrb, Rxrg, Nr2f2, Nr2f1, Nr2c1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1381 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1055 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 604 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 175 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pbx2, Onecut1, Bbx

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 174 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 102 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 101 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 95 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Ets1, Sfpi1, Erf, Bcl11a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 86 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 35 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores