60_testis_A

In [1]:

# Parameters
sample_name = "testis;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_60-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_60-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 18:09:09,136 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	testis
Cell Group	Other Tissues
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	48630	30567	6.2186	54487274	2751281	0.0505	4037474	0.0741	18207607	0.3343

Modelling Metadata

Metric	Value
auPRC	0.7878
Calibrated Recall at 50% FDR	0.126
Number of Positive Examples in Test Data	36968
Number of Negative Examples in Test Data	8033883
Imbalance Ratio in Test Data	0.0046
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

Shared Motifs

Motif Name	Modisco	Homer
Pbx3
Rfx1

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Sp3		absent
Ctcfl		absent
Rfx8		absent
Zfx		absent
Creb1		absent
Creb3		absent
Mbtps2		absent
Smarcc2		absent
Tcfeb		absent
Gabpa		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Hes7	absent
Erf	absent
Zfp143	absent
Yy1	absent
E4f1	absent
E2f1	absent
Klf5	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_60-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_60-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_60-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 21, # seqlets: 14735, Positive for: testis;A;CL

pattern_0: # seqlets: 1761
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp5 , Sp2 , Klf16 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1718
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Gabpa , Ets2 , Erf , Erg , Etv5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1403
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1 , Dux
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1358
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb1 , Jdp2 , 9430076C15Rik , Atf2 , Atf7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1343
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1155
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zfx , Tcfap2d , Wt1 , Egr4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 820
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Tcfap2d , Ctcfl , Zbtb7a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 817
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Klf16 , Sp2 , Sp8 , Maz
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 803
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Yy1 , Sp3 , Wt1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 571
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 540
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcfl , Ctcf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 484
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Zfx , Sp3 , E2f1 , Zbtb7a , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 440
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 409
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx8 , Rfx5 , Zfp740 , Rfx3 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 287
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Bach2 , Sp3 , Tcfec , Mitf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 290
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , Atf7 , Crem , Atf2 , Dbp
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 197
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Mybl2 , Maz , Zbtb7a , Mybl1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 174
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 86
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 43
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_20: # seqlets: 36
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_60-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_60-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_60-naivegw

No motifs with negative importance