In [1]:
# Parameters
sample_name = "iNKT;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_136-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_136-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 21:59:23,641 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeInvariant NKT (iNKT) cells
    Cell GroupOther Immune Cells
    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
    rep11270599692215.63941970341544511330.226131924890.162269464790.3529
    rep21270599692218.68841639073351074560.31236178590.22160488240.3695
    rep31270599692211.62823191805860071250.188347184520.1479112823920.3537
    Modelling Metadata
    MetricValue
    auPRC0.5869
    Calibrated Recall at 50% FDR0.228
    Number of Positive Examples in Test Data108873
    Number of Negative Examples in Test Data7961978
    Imbalance Ratio in Test Data0.0135
    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
Irf1
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Sp3absent
Mbtps2absent
Creb3absent
Runx2absent
Relaabsent
Rfx1absent
Fosabsent
Smarcc2absent
Lef1absent
Tcfebabsent
Gata2absent
Mef2dabsent
Klf16absent
Tcf7l1absent
Ergabsent
Foxi1absent
Unique Homer Motifs
Motif NameModiscoHomer
Ets1absent
Pbx3absent
Zfp143absent
Klf5absent
Runx1absent
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_136-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_136-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_136-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 23, # seqlets: 24635, Positive for: iNKT;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_136-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_136-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_136-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 18, # seqlets: 7523, Negative for: iNKT;A;GEO
  • pattern_0: # seqlets: 2819 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Glis2, Glis1, Zbtb7a, Gli1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1264 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1004 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Neurod1, Atoh8, Atoh1, Tal1, Tcfap4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 936 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 386 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1, Runx2, Runx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 203 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Wt1, Zbtb7a, Sp2, E2f1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 157 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 119 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Ets1, Etv5, Etv6, Elk3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 91 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcfl, Ctcf, Sp3, Wt1, Zfx

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 91 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 88 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 84 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Fos, Smarcc1, Fosb, Jund, Nfe2l2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 65 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 47 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Egr2, Hif3a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Zbtb7a, Zfx, E2f1, Egr4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfic

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 47 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 34 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pax5, Sp3

    SequenceContrib ScoresHyp_Contrib Scores