GenPlay File Formats - Revision history

Nicolas: /* Example */

2013-10-07T15:12:07Z

‎Example

2013-10-07T13:33:52Z

‎Example

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‎Usage

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‎Usage

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‎Usage

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‎Usage

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‎Usage

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‎Usage

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‎Usage

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‎Usage

@@ Line 76: / Line 76: @@
 Here is an example of a bed file.
-  track type=bed
+  track type=bed geneDBURL="<nowiki>http://genome.ucsc.edu/cgi-bin/hgGene?org=Human&hgg_chrom=none&db=hg19&hgg_gene=</nowiki>"
   chr1	11873	14409	uc001aaa.3	0	+	11873	11873	0	3	354,109,1189,	0,739,1347,
   chr1	11873	14409	uc010nxq.1	0	+	12189	13639	0	3	354,127,1007,	0,721,1529,

@@ Line 77: / Line 77: @@
   track type=bed
-  searchURL="<nowiki>http://genome.ucsc.edu/cgi-bin/hgGene?org=Human&hgg_chrom=none&db=hg19&hgg_gene=</nowiki>"
+  geneDBURL="<nowiki>http://genome.ucsc.edu/cgi-bin/hgGene?org=Human&hgg_chrom=none&db=hg19&hgg_gene=</nowiki>"
   chr1	11873	14409	uc001aaa.3	0	+	11873	11873	0	3	354,109,1189,	0,739,1347,
   chr1	11873	14409	uc010nxq.1	0	+	12189	13639	0	3	354,127,1007,	0,721,1529,

@@ Line 363: / Line 363: @@
 === Usage ===
-A wiggle file can generate fixed or variable windows tracks as well as stripes.
+A wiggle file can generate fixed or variable window tracks as well as stripes.
 Be sure that the file extension is '.wig' or that the file starts with the following line:
   track type=wiggle

@@ Line 263: / Line 263: @@
 === Usage ===
-A PSL file can generate stripes. It can also be loaded as a fixed windows, a variable windows, a gene or a repeat track.
+A PSL file can generate stripes. It can also be loaded as a fixed window, a variable window, a gene or a repeat track.
 To be loaded a PSL file needs either to have a '.psl' extension or to have the following first line:

@@ Line 232: / Line 232: @@
 === Usage ===
-The pair files can generate fixed windows tracks.
+The pair files can generate fixed window tracks.
 The file needs to have a '.pair' extension to be loaded in GenPlay.

@@ Line 208: / Line 208: @@
 === Usage ===
-Stripes, fixed and variable windows, repeat and gene tracks can be generated from a GTF file.
+Stripes, fixed and variable window, repeat and gene tracks can be generated from a GTF file.
 A GTF files must either have a '.gtf' extension or to have the following first line:

@@ Line 194: / Line 194: @@
 === Usage ===
-GFF files can be used to load repeats, variable and fixed windows track as well as stripes.
+GFF files can be used to load repeats, variable and fixed window track as well as stripes.
 A GFF file needs to have a '.gff' extension or to have the following first line:

@@ Line 133: / Line 133: @@
 === Usage ===
-The Eland Extended files can generate fixed windows tracks.
+The Eland Extended files can generate fixed window tracks.
 The file needs to have a '.elx' extension or to start with the following line:

@@ Line 111: / Line 111: @@
 === Usage ===
-BedGraph files can be used to load fixed windows and variable windows track.
+BedGraph files can be used to load fixed window and variable window track.
 They can also be loaded as stripes

@@ Line 88: / Line 88: @@
 === Usage ===
 A Bed file with the first 3 required fields can generate stripes.
-If the first four required fields are specified, the file can be loaded as a fixed windows, a variable windows or a repeat track.
+If the first four required fields are specified, the file can be loaded as a fixed window, a variable window or a repeat track.
 If all the fields are specified the file can also be loaded as a gene track.