In [1]:
# Parameters
sample_name = "CH12_QNTPLE;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_90-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_90-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 19:42:20,685 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typech12 with quintuple mt
    Cell GroupCancer or Immortalized 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
    rep1820595425012.41372878645133512920.116530903040.107499002390.3442
    rep2820595425017.68271838017524954460.135924362010.132761200590.3333
    Modelling Metadata
    MetricValue
    auPRC0.5918
    Calibrated Recall at 50% FDR0.205
    Number of Positive Examples in Test Data60313
    Number of Negative Examples in Test Data8010538
    Imbalance Ratio in Test Data0.0075
    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
Pbx3
Bcl11a
Sp3
Ctcf
Tbpl2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Klf16absent
Rfx1absent
Runx1absent
Irf1absent
Nfe2l2absent
Mbtps2absent
Creb3absent
Bach2absent
Smarcc2absent
Mef2aabsent
Hsf1absent
Etv6absent
Ebf1absent
Relbabsent
Unique Homer Motifs
Motif NameModiscoHomer
Yy1absent
E4f1absent
Zfp143absent
Nfkb1absent
Ctcflabsent
Sfpi1absent
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_90-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_90-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_90-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 21, # seqlets: 25355, Positive for: CH12_QNTPLE;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_90-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_90-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_90-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 33, # seqlets: 6835, Negative for: CH12_QNTPLE;A;CL
  • pattern_0: # seqlets: 1669 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1199 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Zbtb7b, Glis1, Zbtb7a, Zic5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 487 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 316 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp637

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 317 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata2, Gata4, Gata1, Gata6, Gata5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 236 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Nr1h2, Esr1, Nr2f2, Hnf4g

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 210 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rfx2, Arid2, Rfx1, Rfx4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 193 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcf15, Bhlha15, Zfp238, Tcf21, Msc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 178 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 177 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 157 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

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

    Zfp637

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 143 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 141 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Maz

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 118 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 115 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 97 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 88 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1, Foxn3, Foxp4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 78 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 74 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Fos, Smarcc1, Nfe2l2, Nfe2, Jund

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 66 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 66 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Sfpi1, Spib

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 65 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hoxa9, Hoxb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 64 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_24: # seqlets: 52 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Jund

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_25: # seqlets: 50 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Klf15, Sp3, Sp2, Maz, E2f1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_26: # seqlets: 48 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_27: # seqlets: 51 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox17, Sox9

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_28: # seqlets: 50 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_29: # seqlets: 45 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Tcfap2d, E2f1, Zfx, E2f3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_30: # seqlets: 33 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_31: # seqlets: 63 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_32: # seqlets: 33 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut2

    SequenceContrib ScoresHyp_Contrib Scores