In [1]:
# Parameters
sample_name = "plasmaB;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_12-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_12-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 15:41:47,629 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeplasma cells
    Cell GroupB 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
    rep115218212710111.534351659011181261520.351103311880.2001196988830.3815
    Modelling Metadata
    MetricValue
    auPRC0.5698
    Calibrated Recall at 50% FDR0.229
    Number of Positive Examples in Test Data143460
    Number of Negative Examples in Test Data7927391
    Imbalance Ratio in Test Data0.0178
    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
Tbpl2
Mbtps2
Stat2
Ctcf
Sp3
Smarcc2
Tcfap2d
Pbx3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Nfiaabsent
Creb3absent
Nfe2absent
Sfpi1absent
Tcfebabsent
Rfx1absent
Mef2aabsent
Hsf1absent
Runx1absent
Ebf1absent
Etv4absent
Nfkb1absent
Ascl2absent
Unique Homer Motifs
Motif NameModiscoHomer
Ferd3labsent
Mef2dabsent
Ets1absent
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_12-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_12-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_12-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 29, # seqlets: 23893, Positive for: plasmaB;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_12-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_12-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_12-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 24, # seqlets: 8635, Negative for: plasmaB;A;CL
  • pattern_0: # seqlets: 2138 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Glis2, Glis1, Zbtb7a, Gli1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1274 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 966 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Dbx1, Pou4f1, Tlx2, Pou1f1, Arid3b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 683 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ahctf1, Arid3b, Onecut1, Phf21a, Dbx1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 461 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637, Hmg20b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 369 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Mesp2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 365 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 352 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 231 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hmg20b, Pou3f4, Pit1, Tlx2, Tbp

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 193 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b, Tbp, Hmg20b, Phf21a, Onecut1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 181 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 179 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tbpl2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 178 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Phf21a, Onecut1, Hmg20b, Onecut3, Ahctf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 165 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 147 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 145 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 124 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 102 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Sfpi1, Ets1, Erg, Fev

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 87 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 73 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 64 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 70 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 45 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 43 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores