In [1]:
# Parameters
sample_name = "TSLEC_SPLND;CD8+A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_119-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_119-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 21:12:44,306 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeSpleen CD8+ T cell(SLEC)
    Cell GroupT cells
    Experiment NameATAC
    Experiment GroupGEO
    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
    rep11137418879516.00872264337061948660.273846447970.205377777340.3438
    rep21137418879516.27772350685264917580.276448802290.207881519960.3471
    rep31137418879515.25242383159451975850.218342200360.177280752390.3391
    Modelling Metadata
    MetricValue
    auPRC0.5924
    Calibrated Recall at 50% FDR0.207
    Number of Positive Examples in Test Data100198
    Number of Negative Examples in Test Data7970653
    Imbalance Ratio in Test Data0.0124
    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
Ctcf
Smarcc2
Ets1
Mbtps2
Pbx3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Sp2absent
Tcfebabsent
Sp3absent
Nfkb1absent
Hsf1absent
Creb3absent
Irf1absent
Rfx1absent
Runx2absent
Fosabsent
Gabpaabsent
Unique Homer Motifs
Motif NameModiscoHomer
Smarcc1absent
Klf2absent
Stat2absent
Runx1absent
Mgaabsent
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_119-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_119-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_119-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 23, # seqlets: 25496, Positive for: TSLEC_SPLND;CD8+A;GEO
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_119-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_119-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_119-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 14, # seqlets: 7233, Negative for: TSLEC_SPLND;CD8+A;GEO
  • pattern_0: # seqlets: 1528 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfkb1, Tbx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1414 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2, Glis1, Zbtb7b, Zic5, Zbtb7a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1376 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 1085 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rela

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 568 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Maz, Sp3, Rreb1, Zfp281, Zfp148

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 268 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, Zbtb7a, Zfx, E2f1, Ctcfl

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 247 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 211 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 208 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5, Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 99 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 94 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Trp63, Hif3a, Mnt

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 51 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata4, Gata1, Gata2, Gata6, Gata3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 45 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 39 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Mnt

    SequenceContrib ScoresHyp_Contrib Scores