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This is a list of synonyms for genomes. This list allows you to match names across diverse quickload sites. For example, if a DAS1 or DAS2 data source (such as ones hosted at Ensembl or UCSC) uses different names to refer to the same genome version, you can specify these in the synonyms.txt. Each line contains any number of synonyms for a genome, separated by tabs.
Here is an example: http://igbquickload.org/quickload/synonyms.txt
Step Four: Create genome.txt files.
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The first column lists the chromosome names and the second column lists their sizes. IGB uses this file to create the sequence selection table under the Data Access Panel.
Here is an example*: *http://igbquickload.org/quickload/A_thaliana_Jun_2009/genome.txt
Note: You can create your genome.txt file from a sequence 2bit file (see below) using twoBitInfo, available from http://hgdownload.cse.ucsc.edu/admin/exe/. See Step Seven: Add sequence data.
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attribute | optional | Description | |||
|---|---|---|---|---|---|
name | Required | The name of the file on your file system. | |||
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 of the file instead. | |||
description | Optional | IGB will display this text as a tooltip when users hover the mouse over the data set title in the Data Access tab. | |||
url | Optional | Use this tag to specify the location of a 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. | |||
load_hint | Optional | Optional but 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. Use this only if your site is the sole provider of a particular genome's reference genome annotations. | |||
label_field | Optional | Use this field to indicate the annotation property (e.g., "score" or "id") that should be used in IGB to label individual annotations. For gene models, "id" is best. | |||
background | Optional | Use this field to define track background color (e.g. background="000000") | |||
foreground | Optional | Use this field to define annotation color (e.g. foreground="00FFFF") | |||
max_depth | Optional | Use this field to define the default max depth value, the number of annotations that can be shown individually (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") | |||
show2tracks | Optional | Use this field to define the default boolean value for the show2Tracks field (e.g. show2tracks="true" or show2tracks="false") | |||
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") | |||
positive_strand_color | Optional | Use this field to define the default positive strand color (e.g. positive_strand_color="CCFFFF") | |||
negative_strand_color | Optional | Use this field to define the default negative strand color (e.g. negative_strand_color="33FFFF") | view_mode | Optional | Use this field to define the default view mode (e.g. view_mode="default", view_mode="depth") |
Step Six: Add your annotation files.
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