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Makefile
Makefile
 
 
Readme.md
Readme.md
 
 
Snakefile
Snakefile
 
 
ZF11_13_peak_annotation_piechart.png
ZF11_13_peak_annotation_piechart.png
 
 
ZF11_13_peak_distance_to_TSS.png
ZF11_13_peak_distance_to_TSS.png
 
 
ZF11_13_peak_upset_plot.png
ZF11_13_peak_upset_plot.png
 
 
ZF11_13_peaks_annotated_nearby_genes.csv
ZF11_13_peaks_annotated_nearby_genes.csv
 
 
ZF13_Nfiabx.png
ZF13_Nfiabx.png
 
 
ZF17_Rbpj.png
ZF17_Rbpj.png
 
 
ZF17_peak_annotation_piechart.png
ZF17_peak_annotation_piechart.png
 
 
ZF17_peak_distance_to_TSS.png
ZF17_peak_distance_to_TSS.png
 
 
ZF17_peak_upset_plot.png
ZF17_peak_upset_plot.png
 
 
ZF17_peaks_annotated_nearby_genes.csv
ZF17_peaks_annotated_nearby_genes.csv
 
 
ZF21_Otx2.png
ZF21_Otx2.png
 
 
ZF27_peak_annotation_piechart.png
ZF27_peak_annotation_piechart.png
 
 
ZF27_peak_distance_to_TSS.png
ZF27_peak_distance_to_TSS.png
 
 
ZF27_peak_upset_plot.png
ZF27_peak_upset_plot.png
 
 
ZF27_peaks_annotated_nearby_genes.csv
ZF27_peaks_annotated_nearby_genes.csv
 
 
ZF29_Otx2.png
ZF29_Otx2.png
 
 
config_human.yaml
config_human.yaml
 
 
config_mouse.yaml
config_mouse.yaml
 
 
nearbyGenes.R
nearbyGenes.R
 
 
nearbyGenes.md
nearbyGenes.md
 
 
peaks_hist.py
peaks_hist.py
 
 
rename.sh
rename.sh
 
 
toMD.py
toMD.py
 
 

Repository files navigation

Quick jump to results

🔎 To jump to nearby genes results: 👉 View detailed nearby gene annotation explanation for ZF11_ZF13 here

MACS2 Peak Counts per Sample

Sample % Alignment N. Reads N. Reads Aligned Narrow Peak Count Broad Peak Count Narrow Peak nolambda
ZF9_Rb_IgG 5.12% 55,327,176 2,833,850 91 196
ZF10_Nfiabx 3.32% 32,876,086 1,091,678 60 317
ZF11_Nfiabx 70.87% 43,919,994 31,126,198 5,149 6,989
ZF12_Rb_IgG 48.06% 36,181,510 17,390,006 233 804
ZF13_Nfiabx 60.88% 34,832,196 21,206,430 8,896 14,695
ZF14_Rb_H3K27me3 89.10% 50,350,514 44,864,458 1,453 4,460 76,749
ZF15_Rbpj 56.14% 46,814,010 26,282,876 208 857
ZF16_Rbpj 69.53% 44,691,678 31,075,740 332 1,122
ZF17_Rbpj 87.87% 37,764,306 33,184,638 20,997 23,731
ZF18_Nr2e3 72.83% 36,322,438 26,455,430 1,004 2,260
ZF19_Rb_IgG 79.41% 59,228,078 47,033,456 1,869 5,271
ZF20_Rb_H3K27me3 74.59% 61,244,308 45,685,172 18,835 48,069
ZF21_Rb_Otx2 51.50% 70,798,026 36,463,584 3,670 6,243
ZF22_Rb_Crx 48.07% 71,001,664 34,129,502 1,704 4,284
ZF23_Rb_Pax6 53.92% 62,726,254 33,824,378 2,6257 29,812
ZF24_Rb_Atoh7 62.34% 62,157,658 38,750,212 5,223 9,811
ZF25_Rb_Isl1 57.98% 62,826,814 36,426,708 6,346 9,331
ZF26_Insm1 65.59% 57,154,524 37,489,690 1,501 4,627
ZF27_neurog2 94.18% 22,878,074 21,545,826 625 1,567
ZF28_nfix 94.81% 26,964,288 25,566,128 1,054 2,301
ZF29_Rb_otx2 95.80% 23,451,770 22,466,858 10,577 15,450
ZF30_Rb_crx 93.57% 34,200,826 32,002,162 15,690 18,103
ZF31_Nrl 94.18% 33,629,112 31,672,562 1,443 2,475
ZF32_Insm1 92.70% 34,757,348 32,221,188 1,033 2,459
ZF33_Insm1 94.74% 29,281,604 27,740,258 1,535 2,598
ZF34_Insm1 94.27% 29,917,384 28,203,072 2,249 3,800

Link to Motif files and contamination Check

View detailed files on Google Drive

Detailed Sample Statistics via flagstats

ZF14_Rb_H3K27me3_stats Statistics

50350514 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
44864458 + 0 mapped (89.10% : N/A)
50350514 + 0 paired in sequencing
25175257 + 0 read1
25175257 + 0 read2
44864458 + 0 properly paired (89.10% : N/A)
44864458 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF11_Nfiabx_stats Statistics

43919994 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
31126198 + 0 mapped (70.87% : N/A)
43919994 + 0 paired in sequencing
21959997 + 0 read1
21959997 + 0 read2
31126198 + 0 properly paired (70.87% : N/A)
31126198 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF10_Nfiabx_stats Statistics

32876086 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
1091678 + 0 mapped (3.32% : N/A)
32876086 + 0 paired in sequencing
16438043 + 0 read1
16438043 + 0 read2
1091678 + 0 properly paired (3.32% : N/A)
1091678 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF27_neurog2_stats Statistics

22878074 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
21545826 + 0 mapped (94.18% : N/A)
22878074 + 0 paired in sequencing
11439037 + 0 read1
11439037 + 0 read2
21545826 + 0 properly paired (94.18% : N/A)
21545826 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF17_Rbpj_stats Statistics

37764306 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
33184638 + 0 mapped (87.87% : N/A)
37764306 + 0 paired in sequencing
18882153 + 0 read1
18882153 + 0 read2
33184638 + 0 properly paired (87.87% : N/A)
33184638 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF15_Rbpj_stats Statistics

46814010 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
26282876 + 0 mapped (56.14% : N/A)
46814010 + 0 paired in sequencing
23407005 + 0 read1
23407005 + 0 read2
26282876 + 0 properly paired (56.14% : N/A)
26282876 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF13_Nfiabx_stats Statistics

34832196 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
21206430 + 0 mapped (60.88% : N/A)
34832196 + 0 paired in sequencing
17416098 + 0 read1
17416098 + 0 read2
21206430 + 0 properly paired (60.88% : N/A)
21206430 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF9_Rb_IgG_stats Statistics

55327176 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
2833850 + 0 mapped (5.12% : N/A)
55327176 + 0 paired in sequencing
27663588 + 0 read1
27663588 + 0 read2
2833850 + 0 properly paired (5.12% : N/A)
2833850 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF28_nfix_stats Statistics

26964288 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
25566128 + 0 mapped (94.81% : N/A)
26964288 + 0 paired in sequencing
13482144 + 0 read1
13482144 + 0 read2
25566128 + 0 properly paired (94.81% : N/A)
25566128 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF12_Rb_IgG_stats Statistics

36181510 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
17390006 + 0 mapped (48.06% : N/A)
36181510 + 0 paired in sequencing
18090755 + 0 read1
18090755 + 0 read2
17390006 + 0 properly paired (48.06% : N/A)
17390006 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF16_Rbpj_stats Statistics

44691678 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
31075740 + 0 mapped (69.53% : N/A)
44691678 + 0 paired in sequencing
22345839 + 0 read1
22345839 + 0 read2
31075740 + 0 properly paired (69.53% : N/A)
31075740 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF18_Nr2e3_stats Statistics


36322438 + 0 in total (QC-passed reads + QC-failed reads)
36322438 + 0 primary
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
26455430 + 0 mapped (72.83% : N/A)
26455430 + 0 primary mapped (72.83% : N/A)
36322438 + 0 paired in sequencing
18161219 + 0 read1
18161219 + 0 read2
26455430 + 0 properly paired (72.83% : N/A)
26455430 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF29_Rb_otx2_stats Statistics

23451770 + 0 in total (QC-passed reads + QC-failed reads)
23451770 + 0 primary
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
22466858 + 0 mapped (95.80% : N/A)
22466858 + 0 primary mapped (95.80% : N/A)
23451770 + 0 paired in sequencing
11725885 + 0 read1
11725885 + 0 read2
22466858 + 0 properly paired (95.80% : N/A)
22466858 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF30_Rb_crx_stats Statistics


34200826 + 0 in total (QC-passed reads + QC-failed reads)
34200826 + 0 primary
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
32002162 + 0 mapped (93.57% : N/A)
32002162 + 0 primary mapped (93.57% : N/A)
34200826 + 0 paired in sequencing
17100413 + 0 read1
17100413 + 0 read2
32002162 + 0 properly paired (93.57% : N/A)
32002162 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF31_Nrl_stats Statistics

33629112 + 0 in total (QC-passed reads + QC-failed reads)
33629112 + 0 primary
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
31672562 + 0 mapped (94.18% : N/A)
31672562 + 0 primary mapped (94.18% : N/A)
33629112 + 0 paired in sequencing
16814556 + 0 read1
16814556 + 0 read2
31672562 + 0 properly paired (94.18% : N/A)
31672562 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF32_Insm1_stats Statistics

34757348 + 0 in total (QC-passed reads + QC-failed reads)
34757348 + 0 primary
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
32221188 + 0 mapped (92.70% : N/A)
32221188 + 0 primary mapped (92.70% : N/A)
34757348 + 0 paired in sequencing
17378674 + 0 read1
17378674 + 0 read2
32221188 + 0 properly paired (92.70% : N/A)
32221188 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF33_Insm1_stats Statistics

29281604 + 0 in total (QC-passed reads + QC-failed reads)
29281604 + 0 primary
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
27740258 + 0 mapped (94.74% : N/A)
27740258 + 0 primary mapped (94.74% : N/A)
29281604 + 0 paired in sequencing
14640802 + 0 read1
14640802 + 0 read2
27740258 + 0 properly paired (94.74% : N/A)
27740258 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF34_Insm1_stats Statistics



29917384 + 0 in total (QC-passed reads + QC-failed reads)
29917384 + 0 primary
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
28203072 + 0 mapped (94.27% : N/A)
28203072 + 0 primary mapped (94.27% : N/A)
29917384 + 0 paired in sequencing
14958692 + 0 read1
14958692 + 0 read2
28203072 + 0 properly paired (94.27% : N/A)
28203072 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF19_Rb_IgG_stats Statistics

59228078 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
47033456 + 0 mapped (79.41% : N/A)
59228078 + 0 paired in sequencing
29614039 + 0 read1
29614039 + 0 read2
47033456 + 0 properly paired (79.41% : N/A)
47033456 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF20_Rb_H3K27me3_stats Statistics

61244308 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
45685172 + 0 mapped (74.59% : N/A)
61244308 + 0 paired in sequencing
30622154 + 0 read1
30622154 + 0 read2
45685172 + 0 properly paired (74.59% : N/A)
45685172 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF21_Rb_Otx2_stats Statistics

70798026 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
36463584 + 0 mapped (51.50% : N/A)
70798026 + 0 paired in sequencing
35399013 + 0 read1
35399013 + 0 read2
36463584 + 0 properly paired (51.50% : N/A)
36463584 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF22_Rb_Crx_stats Statistics

71001664 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
34129502 + 0 mapped (48.07% : N/A)
71001664 + 0 paired in sequencing
35500832 + 0 read1
35500832 + 0 read2
34129502 + 0 properly paired (48.07% : N/A)
34129502 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF23_Rb_Pax6_stats Statistics

62726254 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
33824378 + 0 mapped (53.92% : N/A)
62726254 + 0 paired in sequencing
31363127 + 0 read1
31363127 + 0 read2
33824378 + 0 properly paired (53.92% : N/A)
33824378 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF24_Rb_Atoh7_stats Statistics

62157658 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
38750212 + 0 mapped (62.34% : N/A)
62157658 + 0 paired in sequencing
31078829 + 0 read1
31078829 + 0 read2
38750212 + 0 properly paired (62.34% : N/A)
38750212 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF25_Rb_Isl1_stats Statistics

62826814 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
36426708 + 0 mapped (57.98% : N/A)
62826814 + 0 paired in sequencing
31413407 + 0 read1
31413407 + 0 read2
36426708 + 0 properly paired (57.98% : N/A)
36426708 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

ZF26_Insm1_stats Statistics

57154524 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
37489690 + 0 mapped (65.59% : N/A)
57154524 + 0 paired in sequencing
28577262 + 0 read1
28577262 + 0 read2
37489690 + 0 properly paired (65.59% : N/A)
37489690 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

📘 More Details

👉 View detailed nearby gene annotation explanation for ZF11_ZF13 here

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