Difference between revisions of "Genome Browser json"
Anna Ryabova (Talk | contribs) (Created page with "The BioUML Genome Browser iframe and be adjusted with settings in json format. Here is the json with comments, describing all fields available for setup. { //Path to gen...") |
Anna Ryabova (Talk | contribs) |
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| − | The BioUML [[Genome | + | The BioUML [[Genome browser iframe]] and be adjusted with settings in json format. |
| − | + | <br> | |
| − | + | All fields available for setup are described by comments below. Note, that to use this json obect as an example, all comments should be romoved.<br> | |
| − | { | + | {<br> |
| − | //Path to genome in BioUML server repository | + | //Path to genome in BioUML server repository<br> |
| − | "sequencePath":"databases/EnsemblHuman100/Sequences/chromosomes GRCh38", | + | "sequencePath":"databases/EnsemblHuman100/Sequences/chromosomes GRCh38",<br> |
| − | //[optional] Track with chromosome to be displayed on top, set "" to hide this track | + | //[optional] Track with chromosome to be displayed on top, set "" to hide this track<br> |
| − | "chromosomeTrack": "databases/EnsemblHuman100/Tracks/Karyotype", | + | "chromosomeTrack": "databases/EnsemblHuman100/Tracks/Karyotype",<br> |
| − | //[optional] Chromosome to be opened first | + | //[optional] Chromosome to be opened first<br> |
| − | "chromosome":"1", | + | "chromosome":"1",<br> |
| − | //[optional] Start position | + | //[optional] Start position<br> |
| − | "from":1234, | + | "from":1234,<br> |
| − | //[optional] End position | + | //[optional] End position<br> |
"to": 5678, | "to": 5678, | ||
// Tracks available for display, | // Tracks available for display, | ||
Revision as of 16:08, 3 February 2022
The BioUML Genome browser iframe and be adjusted with settings in json format.
All fields available for setup are described by comments below. Note, that to use this json obect as an example, all comments should be romoved.
{
//Path to genome in BioUML server repository
"sequencePath":"databases/EnsemblHuman100/Sequences/chromosomes GRCh38",
//[optional] Track with chromosome to be displayed on top, set "" to hide this track
"chromosomeTrack": "databases/EnsemblHuman100/Tracks/Karyotype",
//[optional] Chromosome to be opened first
"chromosome":"1",
//[optional] Start position
"from":1234,
//[optional] End position
"to": 5678,
// Tracks available for display,
// Each track is set as "Label":"Path to track in BioUML server repository"
// BigBed tracks can be shown by http/https links
"tracks":{
"GC content":"databases/EnsemblHuman100/Tracks/GC content",
"Genes":"databases/EnsemblHuman100/Tracks/Genes",
"Extended genes":"databases/EnsemblHuman100/Tracks/ExtendedGeneTrack",
"Transcripts":"databases/EnsemblHuman100/Tracks/Transcripts"
},
//Some specific track properties, set {} if no specific properties required
"trackProperties":{
"BBTrack_1":{"chr_name_mapping":"hg38_ucsc_to_ensembl"}
},
//[optional] Tracks visible when browser is opened, by labels in 'tracks' field
//if not set, first two tracks will be shown
"initialTracks": ["Genes", "Transcripts"]
}
