In [1]:
# Parameters
sample_name = "SHRT_TRM_HSC;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_76-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_76-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 18:57:53,177 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeShort Term HSC
    Cell GroupOther Immune 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
    rep11330309693910.22352003678637179140.185735393820.176873523650.3673
    rep21330309693917.69452515135963518000.252747520930.189188874090.3536
    Modelling Metadata
    MetricValue
    auPRC0.6075
    Calibrated Recall at 50% FDR0.195
    Number of Positive Examples in Test Data112530
    Number of Negative Examples in Test Data7958321
    Imbalance Ratio in Test Data0.0139
    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
Sp3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Elk3absent
Nfe2l2absent
Ergabsent
Runx2absent
Sfpi1absent
Nfiaabsent
Mbtps2absent
Smarcc2absent
Rfx1absent
Irf1absent
Zfxabsent
Gata6absent
Creb1absent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Yy1absent
Etv6absent
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_76-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_76-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_76-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 18, # seqlets: 23121, Positive for: SHRT_TRM_HSC;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_76-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_76-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_76-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 18, # seqlets: 7821, Negative for: SHRT_TRM_HSC;A;CL
  • pattern_0: # seqlets: 1861 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rxrg, Rxrb, Nr2f1, Nr2f2, Nr2c1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1446 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1275 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 519 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata2, Gata6, Gata4, Gata5, Gata1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 455 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Twist2, Bhlha15, Msc, Bhlhe23, Neurod2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 422 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Ets1, Etv5, Etv6, Fli1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 383 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 335 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 234 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 157 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 132 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 124 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 109 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox9, Sox17, Sox6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 100 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx2, Runx1, Runx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 92 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, Nr5a2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 70 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 58 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 49 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1, Nr5a1, Esr2

    SequenceContrib ScoresHyp_Contrib Scores