In [1]:
# Parameters
sample_name = "ePyramidal_NRN;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_174-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_174-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 00:05:22,881 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeexcitatory pyramidal neurons
    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
    rep12715772018269.2944102616700286563060.279390552600.0883423531860.4128
    rep22715772018269.394189229958253173750.283876928210.0862373315700.4185
    Modelling Metadata
    MetricValue
    auPRC0.5855
    Calibrated Recall at 50% FDR0.28
    Number of Positive Examples in Test Data247169
    Number of Negative Examples in Test Data7823682
    Imbalance Ratio in Test Data0.0306
    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
Pbx3
Fos
Dbp
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Egr2absent
Mbtps2absent
Tal1absent
Rorcabsent
Gabpaabsent
Rfx1absent
Mef2aabsent
Tbx2absent
Creb3absent
Tbx20absent
Unique Homer Motifs
Motif NameModiscoHomer
Mef2dabsent
Elk3absent
Smarcc2absent
Egr3absent
Nficabsent
E4f1absent
Rfx2absent
Neurog1absent
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_174-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_174-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_174-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 17, # seqlets: 25804, Positive for: ePyramidal_NRN;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_174-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_174-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_174-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 24, # seqlets: 14091, Negative for: ePyramidal_NRN;A;GEO
  • pattern_0: # seqlets: 4044 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 3069 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pou4f3, Pit1, Dbx1, Pou1f1, Pou3f4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1896 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Snai2, Zeb1, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1328 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 995 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut1, Onecut3, Onecut2, Cux2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 551 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr6a1, Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 474 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp238, Bhlha15, Tcf4, Tcf21, Twist2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 314 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1, Nr5a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 275 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1, Foxp4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 217 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 107 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp281, Bcl6, Zfp148, Maz, Sp3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 93 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Klf1, Klf4, Klf8, Klf2, Klf12

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 89 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 89 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, Obox5, AC189028.1, Pitx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 70 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 63 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 73 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Irf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 59 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 58 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Sfpi1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 55 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 51 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Irf1, Sfpi1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Fos, Smarcc1, Fosb, Batf, Junb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 42 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 35 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores