65_eye-NRL_RTN_A

In [1]:

# Parameters
sample_name = "eye-NRL_RTN;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_65-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_65-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 18:23:59,388 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Eye- Neural retina
Cell Group	Neural Cells and 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	44551	31029	8.2759	46621271	2562967	0.055	3658578	0.0785	15749885	0.338

Modelling Metadata

Metric	Value
auPRC	0.7261
Calibrated Recall at 50% FDR	0.166
Number of Positive Examples in Test Data	33039
Number of Negative Examples in Test Data	8037812
Imbalance Ratio in Test Data	0.0041
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
Sp3
Ctcf

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Creb3		absent
Mbtps2		absent
Foxi1		absent
Smarcc2		absent
Ets1		absent
Crx		absent
Mef2d		absent
Tcfeb		absent
Rfx1		absent
Tbpl2		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Klf16	absent
Pbx3	absent
Zfp143	absent
Gabpa	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_65-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_65-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_65-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 20, # seqlets: 17034, Positive for: eye-NRL_RTN;A;CL

pattern_0: # seqlets: 2427
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcf , Ctcfl
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 1985
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Klf16 , Sp5 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 1691
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 1675
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ets1 , Gabpa , Elk3 , Elk1 , Nr2c2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1598
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Foxi1 , Pbx3 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1556
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp5 , Maz , Klf16 , Sp2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 883
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Creb3 , Jdp2 , Atf7 , Creb1 , E4f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 827
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 822
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tcfeb , Bach2 , Mitf , Tcfe3 , Tcfec
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 763
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Crx , Dmbx1 , Gsc2 , Otx2 , Otx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 746
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Tbx2 , Zfp143 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 633
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Wt1 , E2f1 , Zfx , Zbtb7a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 382
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx7
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 350
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zfx , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 235
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Ctcfl , E2f1 , Zfx , Zbtb7a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 167
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Zbtb7a , E2f1 , Wt1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 103
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mef2d , Mef2b , Mef2c , Mef2a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 88
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , E2f1 , Zbtb7a , Wt1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_18: # seqlets: 56
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tbpl2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_19: # seqlets: 47
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , E2f1 , Zbtb7a , Sp2 , Wt1
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_65-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_65-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_65-naivegw

No motifs with negative importance