Mercurial > repos > iuc > bedtools

comparison unionBedGraphs.xml @ 26:c0fbce5dc84a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
author iuc
date Mon, 17 Oct 2016 10:13:20 -0400
parents a2d4c30ba2f9
children b0d5e752c0c5
comparison
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25:6c6963cf9136 26:c0fbce5dc84a
103 <![CDATA[ 103 <![CDATA[
104 **What it does** 104 **What it does**
105 105
106 This tool merges multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files. 106 This tool merges multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files.
107 107
108 .. image:: http://people.virginia.edu/~arq5x/files/bedtools-galaxy/ubg.png
109
110
111 .. class:: warningmark 108 .. class:: warningmark
112 109
113 This tool requires that each BedGraph file is reference-sorted (chrom, then start) and contains non-overlapping intervals (within a given file). 110 This tool requires that each BedGraph file is reference-sorted (chrom, then start) and contains non-overlapping intervals (within a given file).
114 111
115 112
133 ------ 130 ------
134 131
135 **Examples using the Zero Coverage checkbox** 132 **Examples using the Zero Coverage checkbox**
136 133
137 Output example (*without* checking "Report regions with zero coverage"):: 134 Output example (*without* checking "Report regions with zero coverage")::
138 135
139 chr1 900 1000 0 60 0 136 chr1 900 1000 0 60 0
140 chr1 1000 1500 10 60 0 137 chr1 1000 1500 10 60 0
141 chr1 1500 1600 0 60 0 138 chr1 1500 1600 0 60 0
142 chr1 1700 1980 0 50 0 139 chr1 1700 1980 0 50 0
143 chr1 1980 2000 0 50 80 140 chr1 1980 2000 0 50 80
146 chr1 2070 2090 20 0 0 143 chr1 2070 2090 20 0 0
147 chr1 2090 2100 20 0 20 144 chr1 2090 2100 20 0 20
148 145
149 146
150 Output example (*with* checking "Report regions with zero coverage"). The lines marked with (*) are not covered in any input file, but are still reported (The asterisk marking does not appear in the file).:: 147 Output example (*with* checking "Report regions with zero coverage"). The lines marked with (*) are not covered in any input file, but are still reported (The asterisk marking does not appear in the file).::
151 148
152 chr1 0 900 0 0 0 (*) 149 chr1 0 900 0 0 0 (*)
153 chr1 900 1000 0 60 0 150 chr1 900 1000 0 60 0
154 chr1 1000 1500 10 60 0 151 chr1 1000 1500 10 60 0
155 chr1 1500 1600 0 60 0 152 chr1 1500 1600 0 60 0
156 chr1 1600 1700 0 0 0 (*) 153 chr1 1600 1700 0 0 0 (*)
158 chr1 1980 2000 0 50 80 155 chr1 1980 2000 0 50 80
159 chr1 2000 2050 20 50 80 156 chr1 2000 2050 20 50 80
160 chr1 2050 2070 20 0 80 157 chr1 2050 2070 20 0 80
161 chr1 2070 2090 20 0 0 158 chr1 2070 2090 20 0 0
162 chr1 2090 2100 20 0 20 159 chr1 2090 2100 20 0 20
163 chr1 2100 247249719 0 0 0 (*) 160 chr1 2100 247249719 0 0 0 (*)
164 161
165 162
166 ------ 163 ------
167 164
168 **Examples adjusting the "Filler value" for no-covered intervals** 165 **Examples adjusting the "Filler value" for no-covered intervals**
169 166
170 The default value is '0', but you can use any other value. 167 The default value is '0', but you can use any other value.
171 168
172 Output example with **filler = N/A**:: 169 Output example with **filler = N/A**::
173 170
174 chr1 900 1000 N/A 60 N/A 171 chr1 900 1000 N/A 60 N/A
175 chr1 1000 1500 10 60 N/A 172 chr1 1000 1500 10 60 N/A
176 chr1 1500 1600 N/A 60 N/A 173 chr1 1500 1600 N/A 60 N/A
177 chr1 1600 1700 N/A N/A N/A 174 chr1 1600 1700 N/A N/A N/A
178 chr1 1700 1980 N/A 50 N/A 175 chr1 1700 1980 N/A 50 N/A
205 **Non-numeric values** 202 **Non-numeric values**
206 203
207 The input BedGraph files can contain any kind of value in the fourth column, not necessarily a numeric value. 204 The input BedGraph files can contain any kind of value in the fourth column, not necessarily a numeric value.
208 205
209 Input Example:: 206 Input Example::
210 207
211 File-1 File-2 208 File-1 File-2
212 chr1 200 300 Sample1 chr1 100 240 0.75 209 chr1 200 300 Sample1 chr1 100 240 0.75
213 chr1 400 450 Sample1 chr1 250 700 0.43 210 chr1 400 450 Sample1 chr1 250 700 0.43
214 chr1 530 600 Sample2 211 chr1 530 600 Sample2
215 212
216 Output Example:: 213 Output Example::
217 214
218 chr1 100 200 0 0.75 215 chr1 100 200 0 0.75
219 chr1 200 240 Sample1 0.75 216 chr1 200 240 Sample1 0.75
220 chr1 240 250 Sample1 0 217 chr1 240 250 Sample1 0
221 chr1 250 300 Sample1 0.43 218 chr1 250 300 Sample1 0.43
222 chr1 300 400 0 0.43 219 chr1 300 400 0 0.43