In [1]:
# Parameters
sample_name = "EPP;A;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_190-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_190-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 01:00:46,819 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeErythroid progenitor primary cell
    Cell GroupOther Immune Cells
    Experiment NameATAC
    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
    rep1645224727612.45272564417433668690.131433760990.131786005710.3356
    rep2645224727611.39892892597233469030.115834295970.118696914510.3353
    Modelling Metadata
    MetricValue
    auPRC0.5581
    Calibrated Recall at 50% FDR0.193
    Number of Positive Examples in Test Data48132
    Number of Negative Examples in Test Data8022719
    Imbalance Ratio in Test Data0.006
    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
Gabpa
Sp3
Mbtps2
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Rfx2absent
Tcfebabsent
Ets1absent
Sp5absent
Smarcc2absent
Foxi1absent
Hsf1absent
Gata6absent
Prdm1absent
Nfiaabsent
Creb3absent
Klf1absent
Nfe2absent
Unique Homer Motifs
Motif NameModiscoHomer
Tbx2absent
Bach1absent
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_190-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_190-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_190-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 19, # seqlets: 21854, Positive for: EPP;A;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_190-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_190-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_190-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 24, # seqlets: 10083, Negative for: EPP;A;En
  • pattern_0: # seqlets: 2337 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2092 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Zbtb7a, E2f1, Sp2, Maz

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1297 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Maz, Rreb1, Zfp148, Zfp281

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 734 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcf15, Atoh1, Msc, Tal1, Neurog1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 517 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut1, Onecut3, Onecut2, Ahctf1, Hmg20b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 419 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox17, Sox6, Sox9, Sox2, Sox3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 329 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

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

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 255 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Klf1, Klf4, Klf2, Klf3, Klf8

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 234 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ahctf1, Hmg20b, Onecut1, Onecut3, Phf21a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 212 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 189 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 160 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 161 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 142 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 128 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 125 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 91 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 88 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 88 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ahctf1, Onecut1, Hmg20b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 49 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 50 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 38 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 34 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfx

    SequenceContrib ScoresHyp_Contrib Scores