In [1]:
# Parameters
sample_name = "aNonTfh;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_26-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_26-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 16:24:29,931 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeactivated non-Tfh (CD4+CD44+CXCR5-PD1-CD25-) WT
    Cell GroupT 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
    rep11069478577011.885855573249113935860.205183330360.15172650350.3108
    Modelling Metadata
    MetricValue
    auPRC0.6142
    Calibrated Recall at 50% FDR0.208
    Number of Positive Examples in Test Data93110
    Number of Negative Examples in Test Data7977741
    Imbalance Ratio in Test Data0.0115
    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
Mbtps2
Smarcc2
Tcfeb
Ctcf
Pbx3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Irf1absent
Fosabsent
Ergabsent
Ets1absent
Gata2absent
Nfkb1absent
Rfx1absent
Sp3absent
Jdp2absent
Runx2absent
Tcf7l2absent
Rfx8absent
Unique Homer Motifs
Motif NameModiscoHomer
Etv1absent
E4f1absent
Klf5absent
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_26-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_26-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_26-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 21, # seqlets: 25125, Positive for: aNonTfh;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_26-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_26-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_26-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 13, # seqlets: 5120, Negative for: aNonTfh;A;CL
  • pattern_0: # seqlets: 2667 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 621 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Scrt1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 556 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 457 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Tcfap2d, Zbtb7a, Zfx, E2f1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 265 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1, Runx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 151 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 79 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 69 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, Pitx3, AC189028.1, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 60 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sfpi1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 52 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 61 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 38 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores