# Parameters
sample_name = "Tfh;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_24-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_24-naivegw/NaiveauPRC.txt"
homer_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_scans"

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 16:18:58,193 [WARNING] git-lfs not installed

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Tfh (CD4+CD44+CXCR5+PD1+CD25-) WT
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	95446	71809	11.5472	48537970	8872593	0.1829	7063388	0.1456	15961408	0.329

Modelling Metadata

Metric	Value
auPRC	0.6169
Calibrated Recall at 50% FDR	0.201
Number of Positive Examples in Test Data	85301
Number of Negative Examples in Test Data	7985550
Imbalance Ratio in Test Data	0.0106
Test Chromosomes	chr2, chr3, chr19

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
Pbx3
Ctcf

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Sp2		absent
Fos		absent
Nfat5		absent
Rela		absent
Nfia		absent
Tbpl2		absent
Smarcc2		absent
Tcfeb		absent
Klf16		absent
Sp3		absent
Creb3		absent
Irf1		absent
Rfx1		absent
Mbtps2		absent
Runx1		absent
Erg		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Elk4	absent
Hivep1	absent
Sp5	absent
Zfp143	absent
E4f1	absent
Yy1	absent
Mbd2	absent
Prdm1	absent
Batf3	absent

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_24-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_24-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_24-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 20, # seqlets: 25347, Positive for: Tfh;A;CL

• pattern_0: # seqlets: 6244

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Ctcf, Ctcfl

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_1: # seqlets: 4461

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Erg, Ets1, Erf, Gabpa, Ets2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_2: # seqlets: 4282

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sp3, Sp5, Sp2, Klf16, Klf5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_3: # seqlets: 1502

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_4: # seqlets: 1384

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Pbx3, Foxi1, Nfya, Ybx1, Dux

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_5: # seqlets: 1022

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Creb3, 9430076C15Rik, Batf3, Atf7, Jdp2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_6: # seqlets: 844

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Irf1, Prdm1, Stat2, Bcl11a, Irf2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_7: # seqlets: 814

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Rfx1, Rfx2, Arid2, Rfx4, Rfx7

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_8: # seqlets: 759

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Smarcc2, Tbx2, Zfp143, Zfp523, Six5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_9: # seqlets: 660

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Klf16, Klf14, Sp8, Sp5, Klf7

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_10: # seqlets: 645

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Fos, Smarcc1, Jund, Fosb, Fosl1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_11: # seqlets: 638

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Mbtps2, Yy1, Sp3, Wt1, E2f1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_12: # seqlets: 560

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Tcfeb, Bach2, Tcfec, Mitf, Tcfe3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_13: # seqlets: 518

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Runx1, Runx2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_14: # seqlets: 395

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Rela, Relb, Nfkb1, Rel, Hivep1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_15: # seqlets: 227

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nfat5, Nfatc1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_16: # seqlets: 167

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Tbpl2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_17: # seqlets: 88

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sp2, Sp3, Sp1, Maz, Klf6

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_18: # seqlets: 83

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sp3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_19: # seqlets: 54

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nfia, Nfix, Nfib, Nfic

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  

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_24-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_24-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_24-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 27, # seqlets: 7697, Negative for: Tfh;A;CL

• pattern_0: # seqlets: 1482

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Stat5b, Zfp143, Nfkb1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_1: # seqlets: 1353

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Glis2, Zbtb7b, Glis1, Zbtb7a, Zic5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_2: # seqlets: 1023

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_3: # seqlets: 503

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Rfx1, Arid2, Rfx2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_4: # seqlets: 402

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Hoxa9, Hoxc9, Hoxd10, Hoxd11, Cdx4

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_5: # seqlets: 402

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Smarcc1, Fos, Fosb, Nfe2l2, Nfe2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_6: # seqlets: 400

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Tal1, Tcf15, Tcf21, Msc, Bhlha15

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_7: # seqlets: 261

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Atoh8, Twist1, Figla, Tcf4, Mesp2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_8: # seqlets: 236

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Foxd3, Foxj1, Foxm1, Foxn3, Foxp4

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_9: # seqlets: 223

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sox9, Sox17, Sox6

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_10: # seqlets: 197

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Pitx2, AC189028.1, Pitx3, Obox5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_11: # seqlets: 157

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nr5a2, Esrrb, Nr6a1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_12: # seqlets: 151

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nr5a2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_13: # seqlets: 137

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_14: # seqlets: 81

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_15: # seqlets: 76

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_16: # seqlets: 71

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Bcl6, Bcl11a, Sfpi1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_17: # seqlets: 81

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Hsf1, Myc, Zfp143

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_18: # seqlets: 87

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nr5a2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_19: # seqlets: 59

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_20: # seqlets: 55

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Bcl6, Sfpi1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_21: # seqlets: 47

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Bcl6

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_22: # seqlets: 46

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Bcl6

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_23: # seqlets: 41

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_24: # seqlets: 43

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Hsf1, Zfp143

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_25: # seqlets: 42

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_26: # seqlets: 41

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sp3, Ctcfl, Zfx, Mtf1, Zbtb7a

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores