In [1]:
# Parameters
sample_name = "Tfh_LCMV;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_23-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_23-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 16:15:38,094 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeTfh from infected with LCMV
    Cell GroupT 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
    rep1967797287710.96153924622574282460.189456784320.1448133349410.3399
    Modelling Metadata
    MetricValue
    auPRC0.5843
    Calibrated Recall at 50% FDR0.217
    Number of Positive Examples in Test Data80787
    Number of Negative Examples in Test Data7990064
    Imbalance Ratio in Test Data0.01
    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
Pbx3
Ctcf
Sp3
Mbtps2
Tcf7l2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Lef1absent
Irf1absent
Gabpaabsent
Hsf1absent
Tbpl2absent
Creb3absent
Sp2absent
Ergabsent
Runx2absent
Smarcc2absent
Relaabsent
Rfx1absent
Tcfebabsent
Fosabsent
Nfiaabsent
Unique Homer Motifs
Motif NameModiscoHomer
Etv1absent
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_23-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_23-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_23-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 24, # seqlets: 25254, Positive for: Tfh_LCMV;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_23-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_23-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_23-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 20, # seqlets: 8084, Negative for: Tfh_LCMV;A;CL
  • pattern_0: # seqlets: 1588 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Glis2, Glis1, Zbtb7a, Zic5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1341 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1044 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Tcf4, Tcf3, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 909 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b, Dbx1, Pit1, Hmg20b, Tlx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 789 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b, Pou4f3, Dbx1, Phf21a, Pit1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 540 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rfx2, Rfx1, Rest

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 469 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gli1, Gli2, Gli3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 236 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Smarcc1, Fos, Bach1, Nfe2l2, Nfe2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 209 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 178 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 139 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 122 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 99 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox9, Sox17, Sox6, Sox2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 102 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 73 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 72 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx2, Runx3, Runx1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 49 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 43 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Zfx, Ctcfl, Sp2, Zbtb7a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 42 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf, Ctcfl, Sp3, Zfx, Tcfap2d

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 40 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores