In [1]:
# Parameters
sample_name = "BCK_SKN;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_168-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_168-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 23:44:13,347 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeMouse back skin
    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
    rep122080517164810.658959488382207387290.348791396500.1537266486700.4481
    Modelling Metadata
    MetricValue
    auPRC0.5868
    Calibrated Recall at 50% FDR0.237
    Number of Positive Examples in Test Data181992
    Number of Negative Examples in Test Data7888859
    Imbalance Ratio in Test Data0.0225
    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
Gabpa
Nfic
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Lhx2absent
Sox3absent
Trp73absent
Smarcc2absent
Tcfap2aabsent
Sp3absent
Lef1absent
Rfx2absent
Foxp4absent
Fosabsent
Cebpdabsent
Wt1absent
Gata6absent
Grhl1absent
Mbtps2absent
Rfx8absent
Tcfebabsent
Irf1absent
Runx2absent
9430076C15Rikabsent
Pbx3absent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Vsx2absent
Fosbabsent
Klf1absent
Nfyaabsent
Sp2absent
Stat1absent
Klf7absent
Tcfcp2absent
E4f1absent
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_168-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_168-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_168-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_0, # patterns: 27, # seqlets: 19729, Positive for: BCK_SKN;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_168-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_168-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_168-naivegw
No motifs with negative importance