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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 path to the file on the Quickload site itself or an absolute 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 the path to the file relative to the genome version directory where the annots.xml file resides. ex) file path filename="bamfiles/treatment.bam" - a directory "bamfiles" must reside in the genome version directory, alongside annots.xml for that genome |
version ex) name="http://www.example.com/bamfiles/treatment.bam" (absolute) If the file is a reference file, such as 2bit, the reference option must be set to "true". | ||
| index | Optional | If the file is a BAM, CRAM, or tabix indexed file, then IGB assumes the index file has the same name as the target file with a standard extension appended. BAM file indexes have extension ".bai", CRAM file indexes have extension ".crai", and tabix indexes have extension ".tbi." However, if the index is in a different location or has a non-standard name, you can specify its location and file name using the index attribute. ex) file path index="indexes/myindex.tbi" ex) absolute URL index="http://www.example.com/indexfile.bai" |
title | Required | User-friendly text IGB will show in the Data Access Panel as the title of the data set. 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. If this value is present, then IGB displays an "info" icon next to the file name. |
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 in this case means: relative to the Quickload root directory. (Note that this is different from how the file attribute works!) 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. Note: IGB stores local copies of files with load_hint "Whole Sequence" for faster access. See Cache tab under Settings. |
label_field | Optional | Use this field to indicate the annotation property (e.g., "score" or "id") used to label individual annotations within a track. To show no label, insert 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. |
| reference | Optional | Set to "true" if the file is a 2bit reference file. |
background | Optional | Use this field to set a track's background color. Set colors using six-digit, hexadecimal triplets. 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. Any annotations exceeding this number will be drawn on top of each in a single row at the top of the track. This is called the "slop" row. If the track is configured to show plus and minus strand features separately, then the "slop row" for minus strand features appears in the bottom row. To allow IGB to show all available annotations use 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 direction_type setting is "color." |