In [1]:
# Parameters
sample_name = "aB_LPS+IL4;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_14-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_14-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 15:49:45,533 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeaB LPS+IL4
    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
    rep1681254465812.53635265231455844300.106153972170.1025169838160.3227
    Modelling Metadata
    MetricValue
    auPRC0.6599
    Calibrated Recall at 50% FDR0.194
    Number of Positive Examples in Test Data52681
    Number of Negative Examples in Test Data8018170
    Imbalance Ratio in Test Data0.0065
    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
Bcl11a
Ctcf
Mbtps2
Tbpl2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Rfx1absent
Sp3absent
Nfkb1absent
Hsf1absent
Foxi1absent
Tcfecabsent
Mef2aabsent
Sfpi1absent
Smarcc2absent
Jdp2absent
Fosabsent
Ergabsent
Runx2absent
Unique Homer Motifs
Motif NameModiscoHomer
Grhl1absent
Klf5absent
Pbx3absent
Elk1absent
Zfp143absent
Mazabsent
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_14-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_14-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_14-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 19, # seqlets: 25421, Positive for: aB_LPS+IL4;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_14-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_14-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_14-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 22, # seqlets: 9878, Negative for: aB_LPS+IL4;A;CL
  • pattern_0: # seqlets: 1698 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Zbtb7b, Glis1, Zbtb7a, Zic5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1386 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Dbx1, Tlx2, Sebox, Arid3b, Nkx6-1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1371 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Nr4a1, Nr4a3, Esrrb, Esrrg

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1115 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rfx1, Arid2, Rfx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 1099 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 596 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 451 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 311 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 274 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 229 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tbx2, Zfp143, Stat5b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 226 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 225 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Smarcc1, Fos, Nfe2l2, Nfe2, Jund

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 121 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 121 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tbpl2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 112 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 95 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Bcl11a, Spic, Spib, Sfpi1

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

    Nr5a2

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

    Bcl6, Maz

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 79 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata4, Gata2, Gata1, Gata6, Gata3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 76 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 63 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 49 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Spib, Sfpi1

    SequenceContrib ScoresHyp_Contrib Scores