In [1]:
# Parameters
sample_name = "ES;D0;D;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_200-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_200-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 01:33:06,866 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeEmbryonic day 0 (stem cell, ES-CJ7)
    Cell GroupES cells and embryonic tissues
    Experiment NameDHS
    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
    rep11862321239268.1646115819715207861250.1795109745710.0948471445000.4071
    Modelling Metadata
    MetricValue
    auPRC0.6019
    Calibrated Recall at 50% FDR0.285
    Number of Positive Examples in Test Data83919
    Number of Negative Examples in Test Data7986932
    Imbalance Ratio in Test Data0.0104
    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
Pbx3
Rest
Sox2
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Gabpaabsent
Hsf1absent
Tcfecabsent
Pou5f1absent
Smarcc2absent
Sp3absent
Esrrbabsent
Bach1absent
Tcfcp2l1absent
Mbtps2absent
Rfx1absent
Unique Homer Motifs
Motif NameModiscoHomer
Tcfebabsent
Tcfcp2absent
Nr5a1absent
Sox9absent
Klf2absent
Zfp143absent
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_200-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_200-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_200-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_0, # patterns: 25, # seqlets: 15674, Positive for: ES;D0;D;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_200-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_200-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_200-naivegw
No motifs with negative importance