In [1]:
# Parameters
sample_name = "BRN;FRNTL_CRTX;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_68-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_68-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 18:33:17,303 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeBrain- Frontal Cortex
    Cell GroupNeural Cells and Tissues
    Experiment NameATAC
    Experiment GroupCasellas Lab
    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
    rep1109956513727.10935281075940917290.077543677480.0827196325340.3719
    Modelling Metadata
    MetricValue
    auPRC0.5957
    Calibrated Recall at 50% FDR0.23
    Number of Positive Examples in Test Data61108
    Number of Negative Examples in Test Data8009743
    Imbalance Ratio in Test Data0.0076
    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
Mbtps2
Pbx3
Rfx1
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Mef2aabsent
Fosabsent
Etv4absent
Egr2absent
Tal1absent
Sp3absent
Nfiaabsent
Wt1absent
Smarcc2absent
Rfx8absent
Creb3absent
Tbpl2absent
Unique Homer Motifs
Motif NameModiscoHomer
E4f1absent
Bhlha15absent
Zfp143absent
Klf5absent
Klf16absent
Mef2cabsent
Mazabsent
Gabpaabsent
Dbpabsent
Nfe2l2absent
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_68-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_68-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_68-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 23, # seqlets: 20834, Positive for: BRN;FRNTL_CRTX;A;CL
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_68-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_68-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_68-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 13, # seqlets: 10835, Negative for: BRN;FRNTL_CRTX;A;CL
  • pattern_0: # seqlets: 2991 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Dbx1, Tlx2, Arid3b, Pou4f3, Pou4f1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2880 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Rarb, Nr2f6, Rara, Rxra

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1876 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1832 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 496 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp238, Tcf21, Tcf15, Bhlha15, Msc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 275 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxm1, Foxd3, Foxp4, Foxj1, Onecut2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 118 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 88 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 82 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Egr2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 70 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 40 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hif3a, Egr2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 41 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores