In [1]:
# Parameters
sample_name = "aNonTfh_mut;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_27-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_27-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 16:27:07,247 [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-) MUT
    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
    rep1885366949813.74164598112780395350.174963028690.1371140630040.306
    Modelling Metadata
    MetricValue
    auPRC0.6141
    Calibrated Recall at 50% FDR0.205
    Number of Positive Examples in Test Data79301
    Number of Negative Examples in Test Data7991550
    Imbalance Ratio in Test Data0.0098
    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
Sp3
Pbx3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Mbtps2absent
Ergabsent
Fosabsent
Runx1absent
Creb3absent
Smarcc2absent
Irf1absent
Nfkb1absent
Rfx1absent
Nfiaabsent
Hsf1absent
Bach2absent
Ets1absent
Unique Homer Motifs
Motif NameModiscoHomer
Mazabsent
Etv4absent
Yy1absent
Zfp143absent
Prdm1absent
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_27-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_27-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_27-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 19, # seqlets: 24886, Positive for: aNonTfh_mut;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_27-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_27-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_27-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 19, # seqlets: 10512, Negative for: aNonTfh_mut;A;CL
  • pattern_0: # seqlets: 2264 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut1, Onecut3, Hmg20b, Arid3b, Phf21a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2168 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis1, Zbtb7b, Glis2, Gli1, Gli2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1838 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1078 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Scrt2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 532 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 411 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Myc, Olig1, Twist2, Bhlha15, Tcf15

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 392 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 317 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxa3, Foxp4, Foxn3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 316 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 312 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox17, Sox6, Sox2, Sox9, Sox3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 252 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Ets1, ENSMUSG00000044690, Etv6, Etv5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 156 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 112 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ebf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 104 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 86 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

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

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 40 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores