In [1]:
# Parameters
sample_name = "BRN;PTMN;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_69-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_69-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 18:36:02,186 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeBrain- Putamen
    Cell GroupNeural Cells and Tissues
    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
    rep11440438367010.28755474897181428460.148854666710.0999216888270.3963
    Modelling Metadata
    MetricValue
    auPRC0.6488
    Calibrated Recall at 50% FDR0.227
    Number of Positive Examples in Test Data99284
    Number of Negative Examples in Test Data7971567
    Imbalance Ratio in Test Data0.0123
    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
Fos
Dbp
Ctcf
Egr2
Meis1
Pbx3
Gabpa
Mef2c
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Pou2f2absent
Zfxabsent
Sox3absent
Sp3absent
Smarcc2absent
9430076C15Rikabsent
Nfiaabsent
Mbtps2absent
Tcfebabsent
Tbpl2absent
Rfx1absent
Unique Homer Motifs
Motif NameModiscoHomer
E4f1absent
Rfx2absent
Zfp143absent
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_69-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_69-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_69-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 26, # seqlets: 21696, Positive for: BRN;PTMN;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_69-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_69-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_69-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 20, # seqlets: 15066, Negative for: BRN;PTMN;A;CL
  • pattern_0: # seqlets: 5931 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 3071 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut1, Ahctf1, Onecut3, Hmg20b, Foxj3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1684 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Mesp2, Id4, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1210 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 1195 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxj3, Foxp4, Foxn3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 300 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b, Tbp, Arid3b, Tlx2, Phf21a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 219 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 196 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Nr6a1, Esrrb, Hnf4g

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 172 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 153 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Cux2, Onecut1, Onecut3, Pax3, Arid3b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 131 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 125 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Fosb, Jund

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 118 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 108 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 102 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 96 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 92 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637

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

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 49 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 65 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores