Reference genome settings¶
This YAML file contains settings for the reference genome. See also:
Possible keys¶
- GenomeBrowserDescr
- Text. Descriptive text that will be displayed in the genome browser section of the main page.
- AnnotMaxViewPortSize
- Value. Maximum viewport (in bp) the genome browser can have in order to show the genome annotation track.
- RefSequenceSumm
- Boolean. If set, a summary track displaying the reference sequence with be included in the genome browser.
- Annotation
Block. Directives for parsing the annotation file (annotation.gff). The block can contain the following keys:
- Format
- Text. File format. Possible values
- GFF = Version 3 GFF file GTF = Version 2 GTF file
.
- GeneFeature
- Text or List. Feature id(s) used to identify genes.
Example: [gene, pseudogene].
- ExonFeature
- Text or List. Feature id(s) used to identify exons.
- GeneNameAttribute
- Text. Attribute id used to identify gene names.
- GeneNameSetAttribute
- Text or List. Attribute id(s) used to identify gene name sets.
Example: [Name,Alias].
- GeneDescriptionAttribute
- Text or List. Attribute id(s) used to identify gene descriptions.
- ExternalGeneLinks
List. Each item in the list specifies a link for a gene to an external url. These links will show up as buttons in the gene popup window. The block can contain the following keys:
- Url
- Text (required). Url for this link.
This may include a token
{Id}
to refer to the unique gene identifier. Example:https://www.google.co.uk/search?q={Id}
. - Name
- Text (required). Display name for this external link.