In [1]:
# Parameters
sample_name = "NPC;mE6;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_173-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_173-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 00:01:28,584 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeneural progenitor cells(mE6)
    Cell GroupNeural Cells and Tissues
    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
    rep12230091686647.3483155399279NANANANANANA
    Modelling Metadata
    MetricValue
    auPRC0.6227
    Calibrated Recall at 50% FDR0.244
    Number of Positive Examples in Test Data113962
    Number of Negative Examples in Test Data7956889
    Imbalance Ratio in Test Data0.0141
    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
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Mef2aabsent
Creb3absent
Ascl2absent
Sp3absent
Rfx1absent
Restabsent
Fosabsent
Nfiaabsent
Pbx3absent
Sox3absent
Pou2f3absent
Smarcc2absent
Erfabsent
Rfx8absent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Rfx2absent
Relaabsent
Sp2absent
E4f1absent
Evx2absent
Myogabsent
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_173-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_173-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_173-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 19, # seqlets: 19498, Positive for: NPC;mE6;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_173-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_173-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_173-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 34, # seqlets: 10822, Negative for: NPC;mE6;A;GEO
  • pattern_0: # seqlets: 2353 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1, Snai2, Id4, Mesp2, Twist1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1031 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1038 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 927 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Sox9, Sox17, Sox6, Sox2, Sox14

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 681 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ppara, Rarb, Rxra, Rara, Nr2f6

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 444 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 436 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 361 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 270 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 253 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 248 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Gata2, Gata4, Gata1, Gata6, Mecom

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 238 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 232 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ets1, Erg, Etv5, Elk3, Elk1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 217 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Onecut1, Foxp4, Onecut3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 186 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 170 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Smad1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 170 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Irf1, Sox12, Sox4, Onecut2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 169 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Nr6a1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 175 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 151 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 143 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2, Hsf1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 138 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tbpl2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 121 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 98 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxp4, Onecut2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_24: # seqlets: 95 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_25: # seqlets: 88 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_26: # seqlets: 62 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_27: # seqlets: 56 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nhlh2, Nhlh1, Scrt2, Tcf4, Tcf3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_28: # seqlets: 49 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ctcf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_29: # seqlets: 47 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_30: # seqlets: 46 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Bcl6, Maz

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_31: # seqlets: 48 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_32: # seqlets: 41 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_33: # seqlets: 40 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores