In [1]:
# Parameters
sample_name = "proB;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_5-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_5-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 15:21:35,460 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeproB cells
    Cell GroupB 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
    rep1105350741118.7815904035772188210.122361673450.1045195090870.3305
    Modelling Metadata
    MetricValue
    auPRC0.5962
    Calibrated Recall at 50% FDR0.21
    Number of Positive Examples in Test Data74715
    Number of Negative Examples in Test Data7996136
    Imbalance Ratio in Test Data0.0093
    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
Common Motifs
Motif NameModiscoHomer
Sfpi1
Ctcf
Mbtps2
Sp3
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Jdp2absent
Rfx1absent
Ascl2absent
Ebf1absent
Bach2absent
Runx2absent
Tbpl2absent
Nfe2absent
Klf16absent
Smarcc2absent
Nfibabsent
Foxi1absent
Gata6absent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Ferd3labsent
Irf7absent
Pbx3absent
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_5-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_5-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_5-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 20, # seqlets: 24242, Positive for: proB;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_5-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_5-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_5-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 17, # seqlets: 4703, Negative for: proB;A;CL
  • pattern_0: # seqlets: 1374 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 942 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 602 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcf15, Atoh1, Msc, Tcfap4, Tal1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 585 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 220 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 201 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 143 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sp3, E2f1, Tcfap2d, Sp2, Zbtb7a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 110 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 81 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 72 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 69 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 64 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 62 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 60 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Bcl11a, Spib, Sfpi1, Erg

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zscan4, Mnt

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 44 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Maz, Sfpi1, Bcl11a, Spib

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 30 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6

    SequenceContrib ScoresHyp_Contrib Scores