In [1]:
# Parameters
sample_name = "aB;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_137-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_137-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 22:02:28,714 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeAct B cell
    Cell GroupB 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
    rep117100413713511.973254039089143438800.265580722110.1494211355590.3913
    rep21710041371358.166483443705154613840.185395625030.1146314085890.3765
    Modelling Metadata
    MetricValue
    auPRC0.575
    Calibrated Recall at 50% FDR0.229
    Number of Positive Examples in Test Data134975
    Number of Negative Examples in Test Data7935876
    Imbalance Ratio in Test Data0.0167
    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
Tbpl2
Batf
Ctcf
Pbx3
Sfpi1
Pax1
Smarcc2
Ebf1
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Klf16absent
Creb3absent
Bcl11aabsent
Mef2dabsent
Sp3absent
Restabsent
Rfx1absent
Hsf1absent
Runx1absent
Mbtps2absent
Relaabsent
Tcfecabsent
Unique Homer Motifs
Motif NameModiscoHomer
Sp5absent
Mbd2absent
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_137-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_137-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_137-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 27, # seqlets: 27137, Positive for: aB;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_137-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_137-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_137-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 19, # seqlets: 8634, Negative for: aB;A;GEO
  • pattern_0: # seqlets: 1786 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Pou4f1, Dbx1, Tlx2, Lmx1b, Dbx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1319 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1048 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7a, Glis2, Glis1, Zbtb7b

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 836 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 664 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcf15, Tcf21, Msc, Zfp238, Ascl2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 482 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox9, Sox17, Sox6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 453 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1, Foxm1, Foxp4, Foxn3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 346 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tbpl2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 316 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 310 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Pitx2, AC189028.1, Pitx3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 220 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 213 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 168 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 169 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 109 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Mef2d, Mef2a, Mef2b, Mef2c

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 67 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 50 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Sfpi1, Spib

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 40 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Maz, Sfpi1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 38 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores