In [1]:
# Parameters
sample_name = "pGMP;A;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_196-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_196-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 01:19:47,516 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeGranulocyte monocyte 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
    rep115958911050715.38552718258086228400.317446254380.1703124221440.4573
    rep215958911050710.79754307147984857750.197150761500.1179176371620.4097
    Modelling Metadata
    MetricValue
    auPRC0.6378
    Calibrated Recall at 50% FDR0.222
    Number of Positive Examples in Test Data133027
    Number of Negative Examples in Test Data7937824
    Imbalance Ratio in Test Data0.0165
    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
Bcl11a
Sfpi1
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Ets1absent
Fevabsent
Mbtps2absent
Foxi1absent
Gabpaabsent
Hsf1absent
Nfe2absent
Cebpbabsent
Smarcc2absent
Restabsent
Sp3absent
Runx1absent
Rfx2absent
Unique Homer Motifs
Motif NameModiscoHomer
E2f3absent
Zfp143absent
Sp2absent
Pbx3absent
E4f1absent
Cebpeabsent
Cebpgabsent
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_196-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_196-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_196-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 22, # seqlets: 28686, Positive for: pGMP;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_196-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_196-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_196-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 23, # seqlets: 10347, Negative for: pGMP;A;En
  • pattern_0: # seqlets: 2445 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1541 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1267 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7a, Klf16, Glis1, Glis3, Sp1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 683 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rfx2, Rfx1, Arid2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 659 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sfpi1, Bcl11a, Erg, Ets1, Etv6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 535 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tal1, Tcf15, Tcf21, Atoh8, Msc

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

    Esrrb, Nr5a1, Esrrg, Nr5a2, Nr6a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 437 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 362 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1, Runx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 280 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Fos, Fosb, Jund, Smarcc1, Nfe2l2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 233 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 229 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Cebpb, Cebpa, Cebpd, Cebpg

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 174 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 173 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 166 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 159 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf, Ctcfl

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 121 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Myc, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 109 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 81 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 73 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 66 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 48 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 32 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata1, Mecom, Gata2, Gata4, Gata6

    SequenceContrib ScoresHyp_Contrib Scores