In [1]:
# Parameters
sample_name = "LRG_INTSTN;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_53-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_53-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 17:45:57,824 [WARNING] git-lfs not installed
In [3]:
display_metadata(sample_name, perf_file, reportfile, sheetname)
    Sample Information
    MetaData NameDescription
    Cell typeLarge 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
    rep11378579204917.486366859308894730.133411126400.166923212550.3481
    rep21378579204913.20971436124923057690.160821755800.151754533750.3802
    rep31378579204911.08752822969347264520.167537156110.1317106853030.3788
    rep41378579204912.15451810747230515200.168726652950.147368517680.3788
    Modelling Metadata
    MetricValue
    auPRC0.5934
    Calibrated Recall at 50% FDR0.194
    Number of Positive Examples in Test Data103084
    Number of Negative Examples in Test Data7967767
    Imbalance Ratio in Test Data0.0128
    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
Hnf4g
Pbx3
Ctcf
Unique TF-MoDISco Motifs
Motif NameModiscoHomer
Smarcc2absent
Tbpl2absent
Hsf1absent
Grhl1absent
Rfx1absent
Hoxb9absent
Mbtps2absent
Nfiaabsent
Sp3absent
Rfx8absent
Fosabsent
Mbd1absent
Irf1absent
Ets1absent
Foxa2absent
Gata4absent
Gabpaabsent
Tcfebabsent
9430076C15Rikabsent
Unique Homer Motifs
Motif NameModiscoHomer
Klf2absent
Mbd2absent
Elk1absent
Creb1absent
Zfp143absent
Tcfap2dabsent
Gata6absent
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_53-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_53-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_53-naivegw
Displaying motifs which has positive importances for the cell type
metacluster_0, # patterns: 25, # seqlets: 19958, Positive for: LRG_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_53-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_53-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_53-naivegw
No motifs with negative importance