Use annots.xml to specify track color, annotation style, and more
An annots.xml file resides in an IGB QuickLoad genome directory. It lists all data files available for that genome.
The file contains one or more file tags, enclosed in a files element. The file tag has attributes that control how the data looks when loaded as new track into IGB. Many options correspond to options you can configure using the Annotation or Graph tabbed panels in IGB.
attribute | optional | Description |
|---|---|---|
name | Required | The name of the file or a URL. The URL can point to any file, anywhere, provided it's accessible via the internet. You can specify the location of the file using an absolute URL or a relative URL. Relative means: relative to the genome version directory where the annots.xml file resides. ex) name="bamfiles/treatment.bam" (relative) name="http://www.example.com/bamfiles/treatment.bam" (absolute) |
title | Optional | User-friendly text IGB will show in the Data Access Panel as the title of the data set. If you don't provide a title, IGB will display the name attribute instead. If you would like IGB to display data set titles in nested folders in the Available Data Sets section of the Data Access panel, insert the folder separator character "/" used under the Unix operating system (a forward slash) into the title. For example, if a file title is RNA-Seq/Treatment/Sample1, then IGB displays the data set named Sample1 inside a named Treatment inside another folder named RNA-Seq. |
description | Optional | IGB displays this text in the tooltip that appears when the mouse hovers over the data set title in the Data Access tab. |
url | Optional | Use this tag to specify the location of an external Web page describing the data set. If provided, IGB will display an "info" icon next to the data set title. When users click the icon, their Web browser will open showing the contents of the URL you provide. You can specify the location of the file using an absolute URL or a relative URL. An absolute URL looks like this: "http://www.example.com" Relative means: relative to the Quickload root directory. For example, to show "About.html" residing inside a genome version directory named E_unicornis_Jun_2009, use relative url "E_unicornis_Jun_2009/About.html" |
load_hint | Optional | If used, its value should be "Whole Sequence". Using this tag will force IGB to load the entire file when users select the genome version, which is usually appropriate only for reference gene model annotations or other equally small data sets. |
label_field | Optional | Use this field to indicate the annotation property (e.g., "score" or "id") used to label individual annotations within a track.The default is none. To find out what annotation properties are available, view the Selection Info for an annotation loaded from the file. To view annotation properties:
Annotation properties are listed in the first column. |
background | Optional | Use this field to set a track's background color. Set colors using six-digit, hexadecimal triplets, but do not include a leading "#" character. For example, to set a white background, use background="FFFFFF". |
foreground | Optional | Use this field to define annotation or graph colors (e.g. foreground="00FFFF"). See above. |
max_depth | Optional | Use this field to define the default maximum stack height for an annotations track. This is the number of annotations shown individually in a stack (e.g., max_depth="10" or max_depth="0" for unlimited) |
name_size | Optional | Use this field to define the default track label name font size (e.g. name_size="12") |
connected | Optional | Use this field to define the default boolean value for the connected field (e.g. connected="true" or connected="false"). The default is "true". This tells IGB to draw lines linking the blocks belonging to compound features assembled from smaller ones. |
show2tracks | Optional | Use this field to define the default boolean value for the show2Tracks field (e.g. show2tracks="true" or show2tracks="false"). If you would like minus and plus strand features to be displayed in the same track, set this to "false." The default is "true." |
direction_type | Optional | Use this field to dictate whether annotations or alignments will be shown using arrows and/or color to indicate direction. (e.g. direction_type="arrow", direction_type="color", direction_type="both", direction_type="none"). The default is "none." |
positive_strand_color | Optional | Use this field to define the default positive strand color (e.g. positive_strand_color="CCFFFF") for when the direction_type setting is "color." |
negative_strand_color | Optional | Use this field to define the default negative strand color (e.g. negative_strand_color="33FFFF") for when the directon_type setting is "color." |