In [1]:
# Parameters
sample_name = "ISP;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_49-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_49-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 17:33:47,992 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeISP (Immature single positive)
    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
    rep11274509465710.61015116969999655530.194864724810.1265178057790.3481
    Modelling Metadata
    MetricValue
    auPRC0.5958
    Calibrated Recall at 50% FDR0.234
    Number of Positive Examples in Test Data106087
    Number of Negative Examples in Test Data7964764
    Imbalance Ratio in Test Data0.0131
    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
Sp3
E2f1
Ctcf
Tcfeb
Ets1
Pbx3
Smarcc2
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Ascl2absent
Mef2aabsent
Jdp2absent
Irf1absent
Mbtps2absent
Tcf7l2absent
Rfx1absent
Zfp281absent
Nfiaabsent
Runx2absent
Unique Homer Motifs
Motif NameModiscoHomer
Mesp2absent
E4f1absent
Lef1absent
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_49-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_49-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_49-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 19, # seqlets: 20802, Positive for: ISP;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_49-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_49-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_49-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 14, # seqlets: 6964, Negative for: ISP;A;CL
  • pattern_0: # seqlets: 2580 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Dbx1, Arid3b, Tlx2, Pou4f1, Pou1f1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1564 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Atoh8

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 752 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1, Runx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 673 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 307 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 259 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcf7l1, Tcf7l2, Lef1

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

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 127 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 104 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 89 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox17, Sox6, Sox9, Sox2, Sox3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 66 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Myc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 59 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 58 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 56 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores