In [1]:
# Parameters
sample_name = "SKN_EPTHL;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_167-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_167-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 23:40:04,229 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeadult skin epithelia
    Cell GroupOther 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
    rep11879441450599.880171745379212262600.295988868340.1239293699260.4095
    Modelling Metadata
    MetricValue
    auPRC0.5873
    Calibrated Recall at 50% FDR0.233
    Number of Positive Examples in Test Data154780
    Number of Negative Examples in Test Data7916071
    Imbalance Ratio in Test Data0.0192
    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
Gabpa
Ctcf
Fos
Gata2
Rela
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Foxf2absent
Mbtps2absent
Grhl1absent
Mef2aabsent
Smarcc2absent
Irf1absent
Tcfap2aabsent
Trp73absent
Pbx3absent
Tbpl2absent
Cebpbabsent
Klf16absent
Nfiaabsent
Rfx5absent
Jdp2absent
Sp3absent
Unique Homer Motifs
Motif NameModiscoHomer
Trp63absent
Klf2absent
Stat1absent
Zfp143absent
9430076C15Rikabsent
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_167-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_167-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_167-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_0, # patterns: 25, # seqlets: 17562, Positive for: SKN_EPTHL;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_167-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_167-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_167-naivegw
No motifs with negative importance