In [1]:
# Parameters
sample_name = "SML_INTSTN;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_52-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_52-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 17:42:38,138 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeSmall Intestine
    Cell GroupOther Tissues
    Experiment NameATAC
    Experiment GroupCasellas Lab
    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
    rep11216707724213.46351054215112555550.119312924160.122838047060.3615
    rep2121670772429.44484454811952021990.116842769540.096159485870.3582
    Modelling Metadata
    MetricValue
    auPRC0.5977
    Calibrated Recall at 50% FDR0.214
    Number of Positive Examples in Test Data86186
    Number of Negative Examples in Test Data7984665
    Imbalance Ratio in Test Data0.0107
    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
Hnf4g
Grhl1
Klf5
Ctcf
Ehf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Fosabsent
Nfiaabsent
Foxa2absent
Smarcc2absent
Creb3absent
Hoxa13absent
Mbtps2absent
Gata1absent
Irf1absent
Unique Homer Motifs
Motif NameModiscoHomer
Zfp143absent
Hoxb13absent
Smarcc1absent
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_52-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_52-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_52-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_0, # patterns: 18, # seqlets: 20828, Positive for: SML_INTSTN;A;CL
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_52-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_52-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_52-naivegw
No motifs with negative importance