In [1]:
# Parameters
sample_name = "ILC1_AbxGRMFree;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_110-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_110-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 20:45:13,684 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeILC1_AbxGermFree
    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
    rep1832106120816.42942196238836409360.165927818010.126876300870.3477
    rep2832106120810.33442952265035491190.120328339190.09697414780.3302
    Modelling Metadata
    MetricValue
    auPRC0.5801
    Calibrated Recall at 50% FDR0.211
    Number of Positive Examples in Test Data69188
    Number of Negative Examples in Test Data8001663
    Imbalance Ratio in Test Data0.0086
    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
Rela
Smarcc1
Mbtps2
Ctcf
Pbx3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Rfx1absent
9430076C15Rikabsent
Nr1d1absent
Ergabsent
Smarcc2absent
Tbpl2absent
Tcfebabsent
Ets1absent
Nfiaabsent
Sp3absent
Irf1absent
Runx2absent
Unique Homer Motifs
Motif NameModiscoHomer
Mbd2absent
Zfp143absent
Elk3absent
Jdp2absent
Sp5absent
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_110-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_110-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_110-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 19, # seqlets: 23205, Positive for: ILC1_AbxGRMFree;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_110-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_110-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_110-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 12, # seqlets: 5056, Negative for: ILC1_AbxGRMFree;A;GEO
  • pattern_0: # seqlets: 1214 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Glis2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 901 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7c, Gli3, Gli1, Gli2, Hic2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 699 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 672 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Snai2, Zeb1, Id4, Mesp2, Scrt2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 440 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Twist2, Olig1, Tcf21, Olig2, Msc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 347 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hoxc9, Hoxa9, Cdx4

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 220 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 197 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5, Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 122 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1, Runx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 100 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 98 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Esrrb

    SequenceContrib ScoresHyp_Contrib Scores