In [1]:
# Parameters
sample_name = "ROD_PHT_RCPTR;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_150-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_150-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.
2019-07-22 22:43:25,559 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typerod photoreceptors
    Cell GroupNeural Cells and Tissues
    Experiment NameATAC
    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
    rep11017108080118.31342711383272293000.266858454810.215796221880.3551
    rep21017108080115.84423378697581077870.240164217350.1902122261990.362
    Modelling Metadata
    MetricValue
    auPRC0.6354
    Calibrated Recall at 50% FDR0.163
    Number of Positive Examples in Test Data86434
    Number of Negative Examples in Test Data7984417
    Imbalance Ratio in Test Data0.0107
    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
Sp3
Gabpa
Ctcf
Crx
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Creb3absent
Rfx8absent
Foxi1absent
Mbtps2absent
Rfx1absent
Rorbabsent
Smarcc2absent
Tcfebabsent
Mef2dabsent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Srebf2absent
9430076C15Rikabsent
Pbx3absent
Yy1absent
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_150-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_150-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_150-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 17, # seqlets: 22644, Positive for: ROD_PHT_RCPTR;A;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_150-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_150-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_150-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 20, # seqlets: 12307, Negative for: ROD_PHT_RCPTR;A;GEO
  • pattern_0: # seqlets: 2259 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp238, Tcf15, Bhlha15, Tcf21, Tcf4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1886 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1848 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1096 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 1029 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Otx1, Obox5, Otx2, Obox6, Pitx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 971 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gli3, Gli1, Gli2, Hic2, Zbtb7b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 877 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pbx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 852 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Esrra, Esrrg, Nr4a2, Nr1h2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 236 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 220 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 158 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 156 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 142 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 133 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 125 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 84 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 72 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 61 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 54 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 48 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores