In [1]:
# Parameters
sample_name = "aB_LPS;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_13-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_13-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 15:46:06,928 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeaB LPS
    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
    rep1559593608913.67354634102445656950.098646697320.1008148931390.3215
    Modelling Metadata
    MetricValue
    auPRC0.6772
    Calibrated Recall at 50% FDR0.168
    Number of Positive Examples in Test Data45734
    Number of Negative Examples in Test Data8025117
    Imbalance Ratio in Test Data0.0057
    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
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Bcl11aabsent
Ebf1absent
Fosabsent
Tbpl2absent
Mef2dabsent
Smarcc2absent
Rfx2absent
Sfpi1absent
Creb3absent
Foxi1absent
Rfx8absent
Sp3absent
Tcfebabsent
Mbtps2absent
Nfkb1absent
Hsf1absent
Unique Homer Motifs
Motif NameModiscoHomer
Klf5absent
Elk1absent
E4f1absent
Zfp143absent
Pbx3absent
Mazabsent
Hivep1absent
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_13-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_13-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_13-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 19, # seqlets: 24052, Positive for: aB_LPS;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_13-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_13-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_13-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 29, # seqlets: 8284, Negative for: aB_LPS;A;CL
  • pattern_0: # seqlets: 2129 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Glis2, Zbtb7a, Glis1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1281 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Scrt1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 973 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Rarb, Nr2f6, Rara, Rxra

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 672 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 452 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp238, Tcf21, Bhlha15, Tcf15, Msc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 432 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gli1, Gli2, Gli3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 270 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 224 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxp4, Foxd3, Foxj3, Foxj1, Foxn3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 202 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Esrrb, Pitx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 181 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 143 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rela

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 124 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Maz, Bcl6, Zfp281, Sp2, Zfp148

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 117 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Fos, Smarcc1, Fosb, Nfe2l2, Nfe2

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

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 98 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143, Myc, Stat5b, Stat5a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 92 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ebf1

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

    Sp3, Zfx, E2f1, Sp2, Zbtb7a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 84 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp2, E2f6, Sp3, E2f1, Klf5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 84 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 82 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 73 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

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

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 67 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 56 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_24: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_25: # seqlets: 39 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_26: # seqlets: 36 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp143, Smarcc2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_27: # seqlets: 35 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Sp2, Wt1, Zbtb7a, E2f1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_28: # seqlets: 30 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores