In [1]:
# Parameters
sample_name = "ILC2+IL33+IL25;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_106-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_106-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 20:31:39,678 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeILC2+IL33+IL25
    Cell GroupOther Immune 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
    rep11162288428113.00113922003464279690.16447283310.1206127511090.3253
    rep21162288428113.23074192839467152490.160246075710.1099133578160.3187
    Modelling Metadata
    MetricValue
    auPRC0.5603
    Calibrated Recall at 50% FDR0.231
    Number of Positive Examples in Test Data97401
    Number of Negative Examples in Test Data7973450
    Imbalance Ratio in Test Data0.0121
    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
9430076C15Rik
Sp3
Pbx3
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Fosabsent
Zfxabsent
Nr4a2absent
Gata4absent
Tcfebabsent
Irf1absent
Smarcc2absent
Rfx8absent
Hsf1absent
Mbtps2absent
Tbpl2absent
Runx2absent
Ets1absent
Rfx1absent
Nfiaabsent
Relaabsent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
E2f1absent
Nfkb1absent
Gabpaabsent
Yy1absent
Prdm1absent
Smarcc1absent
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_106-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_106-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_106-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 25, # seqlets: 22833, Positive for: ILC2+IL33+IL25;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_106-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_106-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_106-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 22, # seqlets: 9292, Negative for: ILC2+IL33+IL25;A;GEO
  • pattern_0: # seqlets: 2202 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 2192 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Arid3b, Lhx3, Prrxl1, Dbx1, Lhx5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1237 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Glis1, Glis2, Zbtb7a, Gli1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 979 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Rarb, Ppara, Nr2f6, Rara, Rxra

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 485 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nfe2l2, Nfe2, Jund, Batf, Fos

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 291 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata2, Gata4, Gata1, Gata6, Gata3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 268 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 205 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 196 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hoxc9, Hoxa9, Pbx2, Cdx4, Hoxb1

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

    Bcl6, Sfpi1, Bcl11a, Spib, Spic

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 140 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 128 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 125 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 109 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Klf1, Runx2, Klf2, Runx3, Gli2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 101 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 88 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Maz

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

    Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 100 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 66 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 48 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 36 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 34 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Zfp143

    SequenceContrib ScoresHyp_Contrib Scores