64_PNCRS_A

In [1]:

# Parameters
sample_name = "PNCRS;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_64-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_64-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 18:21:46,508 [WARNING] git-lfs not installed

In [3]:

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	pancreas
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	36020	20104	11.3049	4730481	93650	0.0199	243720	0.0517	1301106	0.2762
rep2	36020	20104	7.4276	42092454	1383081	0.0329	2289961	0.0544	12429786	0.2954

Modelling Metadata

Metric	Value
auPRC	0.6528
Calibrated Recall at 50% FDR	0.21
Number of Positive Examples in Test Data	24452
Number of Negative Examples in Test Data	8046399
Imbalance Ratio in Test Data	0.003
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
Jdp2
Sp3
Pbx3

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Mbtps2		absent
Hsf1		absent
Smarcc2		absent
Fos		absent
Irf9		absent
Erf		absent
Rfx1		absent
Rfx8		absent
Ctcfl		absent
Irf1		absent
Tbpl2		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Elk4	absent
Zfp143	absent
Yy1	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_64-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_64-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_64-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 18, # seqlets: 19752, Positive for: PNCRS;A;CL

pattern_0: # seqlets: 4894
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Sp2 , Sp5 , Klf16 , Klf5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_1: # seqlets: 2750
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Erf , Etv5 , Erg , Gabpa , Elk3
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_2: # seqlets: 2588
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Jdp2 , Thrb , Creb3 , Creb1 , E4f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_3: # seqlets: 2572
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Pbx3 , Foxi1 , Nfya , Ybx1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_4: # seqlets: 1809
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_5: # seqlets: 1335
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Mbtps2 , Sp3 , Yy1 , Wt1 , E2f1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_6: # seqlets: 1249
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Ctcfl , Ctcf
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_7: # seqlets: 1008
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Smarcc2 , Zfp143 , Tbx2 , Zfp523 , Six5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_8: # seqlets: 457
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sp3 , Zfx , E2f1 , Zbtb7a
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_9: # seqlets: 283
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf1 , Prdm1 , Bcl11a , Stat2 , Irf2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_10: # seqlets: 226
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Fos , Smarcc1 , Jund , Fosb , Nfe2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_11: # seqlets: 160
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx1 , Rfx2 , Arid2 , Rfx4 , Rfx5
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_12: # seqlets: 97
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Rfx8 , Rfx3 , Rfx5 , Rfx7 , Rfx4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_13: # seqlets: 93
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Hsf1
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_14: # seqlets: 85
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Irf9 , Irf5 , Stat2 , Irf2 , Irf4
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_15: # seqlets: 70
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Tbpl2
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_16: # seqlets: 39
Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :
Sequence
Contrib Scores
Hyp_Contrib Scores
pattern_17: # seqlets: 37
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_64-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_64-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_64-naivegw

No motifs with negative importance