In [1]:
# Parameters
sample_name = "DC_LPS;2h;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_147-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_147-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 22:34:00,119 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typedendritic cell(100 ng/mL Lipopolysaccharide, 2hours)
    Cell GroupOther Immune 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
    rep11769691245426.8918178032455557380.06849726020.0608271690780.3323
    rep217696912454212.558350076735174416920.348484841300.1695218372550.4362
    Modelling Metadata
    MetricValue
    auPRC0.6374
    Calibrated Recall at 50% FDR0.191
    Number of Positive Examples in Test Data160875
    Number of Negative Examples in Test Data7909976
    Imbalance Ratio in Test Data0.0199
    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
Sp3
Fos
Pbx3
Sfpi1
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Cebpbabsent
Smarcc2absent
Hsf1absent
Irf1absent
Runx2absent
Erfabsent
Rfx1absent
Tbpl2absent
Ergabsent
Relbabsent
Tcfecabsent
Creb3absent
Unique Homer Motifs
Motif NameModiscoHomer
Runx1absent
Jdp2absent
Relabsent
Bcl11aabsent
Zfp143absent
Yy1absent
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_147-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_147-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_147-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 21, # seqlets: 24034, Positive for: DC_LPS;2h;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_147-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_147-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_147-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 22, # seqlets: 10567, Negative for: DC_LPS;2h;A;GEO