In [1]:
# Parameters
sample_name = "GC_B;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_11-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_11-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 15:38:46,967 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeGC B cells
    Cell GroupB cells
    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
    rep113496211075910.260548983482146872250.391579540.187185473240.3788
    Modelling Metadata
    MetricValue
    auPRC0.6025
    Calibrated Recall at 50% FDR0.196
    Number of Positive Examples in Test Data120801
    Number of Negative Examples in Test Data7950050
    Imbalance Ratio in Test Data0.015
    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
Common Motifs
Motif NameModiscoHomer
Sfpi1
Tbpl2
Sp2
Ctcf
Smarcc2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Foxi1absent
Sp3absent
Bcl11aabsent
Pax5absent
Rfx8absent
Mbtps2absent
Rfx1absent
Mef2aabsent
Creb3absent
Relbabsent
Ets1absent
Ebf1absent
Elk3absent
Tcfebabsent
Unique Homer Motifs
Motif NameModiscoHomer
Irf1absent
Atf6absent
Yy1absent
Pbx3absent
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_11-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_11-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_11-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 22, # seqlets: 25644, Positive for: GC_B;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_11-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_11-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_11-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 16, # seqlets: 4216, Negative for: GC_B;A;CL
  • pattern_0: # seqlets: 1060 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Glis1, Zbtb7b, Zic5, Zbtb7a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 638 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 461 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Rarb, Rxra, Nr4a1, Esrrg

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 400 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 332 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox9, Sox6, Sox17

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 287 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 228 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 170 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 128 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ets1, Erg, Etv5, Elk3, Etv6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 121 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 79 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 72 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 68 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 70 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 59 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 43 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Maz, Rreb1, Sp3, Zfp281, Zfp148

    SequenceContrib ScoresHyp_Contrib Scores