1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
|
.. _unionbedg:
###############
*unionbedg*
###############
**bedtools unionbedg** combines multiple BEDGRAPH files into a single file such that one can directly
compare coverage (and other text-values such as genotypes) across multiple sample
==========================================================================
Usage and option summary
==========================================================================
Usage:
::
bedtools unionbedg [OPTIONS] -i FILE1 FILE2 FILE3 ... FILEn
=========================== ===============================================================================================================================================================================================================
Option Description
=========================== ===============================================================================================================================================================================================================
**-header** Print a header line, consisting of chrom, start, end followed by the names of each input BEDGRAPH file.
**-names** A list of names (one per file) to describe each file in -i. These names will be printed in the header line.
**-empty** Report empty regions (i.e., start/end intervals w/o values in all files). *Requires the '-g FILE' parameter (see below)*.
**-g** The genome file to be used to calculate empty regions.
**-filler TEXT** Use TEXT when representing intervals having no value. Default is '0', but you can use 'N/A' or any other text.
**-examples** Show detailed usage examples.
=========================== ===============================================================================================================================================================================================================
==========================================================================
Default behavior
==========================================================================
::
cat 1.bg
chr1 1000 1500 10
chr1 2000 2100 20
cat 2.bg
chr1 900 1600 60
chr1 1700 2050 50
cat 3.bg
chr1 1980 2070 80
chr1 2090 2100 20
cat sizes.txt
chr1 5000
bedtools unionbedg -i 1.bg 2.bg 3.bg
chr1 900 1000 0 60 0
chr1 1000 1500 10 60 0
chr1 1500 1600 0 60 0
chr1 1700 1980 0 50 0
chr1 1980 2000 0 50 80
chr1 2000 2050 20 50 80
chr1 2050 2070 20 0 80
chr1 2070 2090 20 0 0
chr1 2090 2100 20 0 20
==========================================================================
``-header`` Add a header line to the output
==========================================================================
::
bedtools unionbedg -i 1.bg 2.bg 3.bg -header
chrom start end 1 2 3
chr1 900 1000 0 60 0
chr1 1000 1500 10 60 0
chr1 1500 1600 0 60 0
chr1 1700 1980 0 50 0
chr1 1980 2000 0 50 80
chr1 2000 2050 20 50 80
chr1 2050 2070 20 0 80
chr1 2070 2090 20 0 0
chr1 2090 2100 20 0 20
==========================================================================
``-names`` Add a header line with custom file names to the output
==========================================================================
::
bedtools unionbedg -i 1.bg 2.bg 3.bg -header -names WT-1 WT-2 KO-1
chrom start end WT-1 WT-2 KO-1
chr1 900 1000 0 60 0
chr1 1000 1500 10 60 0
chr1 1500 1600 0 60 0
chr1 1700 1980 0 50 0
chr1 1980 2000 0 50 80
chr1 2000 2050 20 50 80
chr1 2050 2070 20 0 80
chr1 2070 2090 20 0 0
chr1 2090 2100 20 0 20
==========================================================================
``-empty`` Include regions that have zero coverage in all BEDGRAPH files.
==========================================================================
::
bedtools unionbedg -i 1.bg 2.bg 3.bg -empty -g sizes.txt -header
chrom start end WT-1 WT-2 KO-1
chrom start end 1 2 3
chr1 0 900 0 0 0
chr1 900 1000 0 60 0
chr1 1000 1500 10 60 0
chr1 1500 1600 0 60 0
chr1 1600 1700 0 0 0
chr1 1700 1980 0 50 0
chr1 1980 2000 0 50 80
chr1 2000 2050 20 50 80
chr1 2050 2070 20 0 80
chr1 2070 2090 20 0 0
chr1 2090 2100 20 0 20
chr1 2100 5000 0 0 0
==========================================================================
``-filler`` Use a custom value for missing values.
==========================================================================
::
bedtools unionbedg -i 1.bg 2.bg 3.bg -empty -g sizes.txt -header -filler N/A
chrom start end WT-1 WT-2 KO-1
chrom start end 1 2 3
chr1 0 900 N/A N/A N/A
chr1 900 1000 N/A 60 N/A
chr1 1000 1500 10 60 N/A
chr1 1500 1600 N/A 60 N/A
chr1 1600 1700 N/A N/A N/A
chr1 1700 1980 N/A 50 N/A
chr1 1980 2000 N/A 50 80
chr1 2000 2050 20 50 80
chr1 2050 2070 20 N/A 80
chr1 2070 2090 20 N/A N/A
chr1 2090 2100 20 N/A 20
chr1 2100 5000 N/A N/A N/A
==========================================================================
Use BEDGRAPH files with non-numeric values.
==========================================================================
::
cat 1.snp.bg
chr1 0 1 A/G
chr1 5 6 C/T
cat 2.snp.bg
chr1 0 1 C/C
chr1 7 8 T/T
cat 3.snp.bg
chr1 0 1 A/G
chr1 5 6 C/T
bedtools unionbedg -i 1.snp.bg 2.snp.bg 3.snp.bg -filler -/-
chr1 0 1 A/G C/C A/G
chr1 5 6 C/T -/- C/T
chr1 7 8 -/- T/T -/-
|
