In [1]:
# Parameters
sample_name = "pCMP;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_194-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_194-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.
2019-07-23 01:13:06,182 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeCommon myeloid progenitor primary cell
    Cell GroupOther Immune Cells
    Experiment NameATAC
    Experiment GroupENCODE
    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
    rep11495309920113.28772598757252832750.203534887340.1343109747900.4226
    rep21495309920114.31732141465546494330.217331222430.145991099330.4258
    Modelling Metadata
    MetricValue
    auPRC0.6136
    Calibrated Recall at 50% FDR0.231
    Number of Positive Examples in Test Data118406
    Number of Negative Examples in Test Data7952445
    Imbalance Ratio in Test Data0.0147
    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
Ctcf
Gata6
Sfpi1
Rest
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Cebpbabsent
Jdp2absent
Mef2aabsent
Mbtps2absent
Foxi1absent
Smarcc2absent
Nfe2absent
Nfiaabsent
Bcl11aabsent
Hsf1absent
Runx2absent
Rfx2absent
Tcfebabsent
Unique Homer Motifs
Motif NameModiscoHomer
Cebpgabsent
Pbx3absent
Zfp143absent
Bach1absent
Creb3absent
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_194-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_194-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_194-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 22, # seqlets: 27634, Positive for: pCMP;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_194-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_194-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_194-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 18, # seqlets: 7398, Negative for: pCMP;A;CL
  • pattern_0: # seqlets: 2886 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut1, Arid3b, Onecut3, Dbx1, Phf21a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 706 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata2, Gata4, Gata1, Gata3, Gata5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 658 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sfpi1, Bcl11a, Etv6, Ets1, Spic

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 591 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 587 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxm1, Foxj1, Foxp4, Onecut2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 464 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp238

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 287 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 202 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    AC189028.1, Pitx2, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 180 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 128 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Irf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 120 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Myc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 106 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Cebpb, Cebpa, Cebpd, Cebpg, Cebpe

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

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 96 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 90 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Mef2a, Mef2c, Mef2b, Mef2d, Tead4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 87 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 80 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 31 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores