1_naiveCD8_A

In [1]:

# Parameters
sample_name = "naiveCD8;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_1-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_1-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 15:10:15,907 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	naive CD8
Cell Group	T cells
Experiment Name	ATAC
Experiment Group	Casellas Lab

Pipeline Output

replicate	Naïve overlap peaks	IDR peaks	TSS enrichment (< 8 is very poor <10 is low)	Final number of unique mapping, dup-filtered, chrM filtered reads	Number of reads in called peak regions	Fraction of reads in called peak regions	Number of reads in promoter regions	Fraction of reads in promoter regions	Number of reads in enhancer regions	Fraction of reads in enhancer regions
rep1	93898	70870	11.888	53664345	7669787	0.143	5612991	0.1046	16388356	0.3055

Modelling Metadata

Metric	Value
auPRC	0.5585
Calibrated Recall at 50% FDR	0.26
Number of Positive Examples in Test Data	76284
Number of Negative Examples in Test Data	7994567
Imbalance Ratio in Test Data	0.0095
Test Chromosomes	chr2, 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

Common Motifs

Motif Name	Modisco	Homer
Sp3
Pbx3
Ctcf
Mbtps2

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Irf1		absent
Nfia		absent
Lef1		absent
Rfx1		absent
Ets1		absent
Runx2		absent
Tcfeb		absent
9430076C15Rik		absent
Fos		absent
Smarcc2		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Gabpa	absent
Zfp143	absent
Creb3	absent

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_1-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_1-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_1-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 18, # seqlets: 22015, Positive for: naiveCD8;A;CL

pattern_0: # seqlets: 5944
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ets1 , Erg , Erf , Etv5 , Etv6
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 4278
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 3045
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp5 , Klf16 , Sp2 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1431
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1142
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1 , Dux
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1126
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Prdm1 , Stat2 , Irf2 , Bcl11a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 994
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
9430076C15Rik , Atf7 , Atf2 , Jdp2 , Creb1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 750
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Runx2 , Runx1 , Runx3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 654
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 631
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 557
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Tcfec , Bach2 , Mitf , Tcfe3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 340
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 334
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Jund , Fosb , Nfe2l2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 302
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Lef1 , Tcf7l2 , Tcf7l1 , Tcf7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 168
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ets1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 144
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 134
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Nfia , Nfix , Nfib , Nfic
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 41
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores

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_1-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_1-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_1-naivegw

No motifs with negative importance