Reference genome settings¶
This YAML file contains settings for the reference genome. See also:
Possible keys¶
- 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.