In [1]:
# Parameters
sample_name = "immatureB;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_7-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_7-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 15:27:44,104 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeimmature B 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
    rep11080318538112.74554966132686287730.173858430080.1177154318410.3109
    Modelling Metadata
    MetricValue
    auPRC0.5535
    Calibrated Recall at 50% FDR0.257
    Number of Positive Examples in Test Data92124
    Number of Negative Examples in Test Data7978727
    Imbalance Ratio in Test Data0.0114
    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
Sfpi1
Pbx3
Smarcc2
Ctcf
Tbpl2
Sp3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Mbtps2absent
Rfx1absent
Sp2absent
Bcl11aabsent
Creb3absent
Ebf1absent
Relbabsent
Mef2dabsent
Nfiaabsent
Unique Homer Motifs
Motif NameModiscoHomer
E4f1absent
Yy1absent
Irf1absent
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_7-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_7-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_7-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 20, # seqlets: 26048, Positive for: immatureB;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_7-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_7-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_7-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 18, # seqlets: 7121, Negative for: immatureB;A;CL
  • pattern_0: # seqlets: 1434 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1046 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pou4f1, Otp, Esx1, Prrx1, Pou3f1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1017 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Nr1h2, Nr6a1, Esrrg, Nr4a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 997 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis1, Zbtb7b, Glis2, Zbtb7a, Zic5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 544 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 497 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcf4, Zeb1, Figla, Twist1, Atoh8

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 351 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp238, Tcf15, Tcf21, Bhlha15, Msc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 351 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hoxc9, Hoxa9, Hoxd8, Hoxd10, Hoxb7

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 192 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 182 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 138 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 65 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb, Nr6a1, Maz, Nr5a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 62 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 61 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 56 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 40 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Smarcc1, Fosb, Fos, Bach1, Jund

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 58 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 30 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Maz

    SequenceContrib ScoresHyp_Contrib Scores