IGB User's Guide
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Code Block
<files>
  <file name="TAIR10.bed.gz" 
   title="TAIR10 ALL" 
   description="All TAIR10 genome models" 
   label_field="id"
   background="000000"
   foreground="00FFFF"
   max_depth="10"
   name_size="12"/>
</files>

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attribute

optional

Description

name

Required

The name of the file on your file system or a URL. The URL can point to any file, anywhere, provided it's accessible via the internet.

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 attribute 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 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 annotationsor other equally small data sets.

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 or graph colors (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 in a stack (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")

Step Six: Add your annotation files.

Place your annotations annotation, BAM, or graph (bedgraph or bigwig) files into the appropriate genome sub-directories. They can be "gzipped" or not depending on your preference. You should be able to use any of the many formats IGB supports.  For annotation files, BED format is the most commonly used.You can you use any format IGB supports. 

Starting with IGB 6.6, IGB QuickLoad can support BED, bedgraph, and GFF files that have been sorted, compressed, and indexed using the bgzip and tabix utility. Doing this helps speed up data loading in IGB and allows loading data by region. For an example of how we used tabix to distribute coverage and junction files from an RNA-Seq data sets from maizeset, see Creating a new genome release for IGB QuickLoad from the IGB Developer's Guide.

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You may not need to do this if you are working with a genome that other QuickLoad or DAS2 sites support. That is, IGB may be able to retrieve sequence data for your genome from other sites if it can recognize that your annotations belong to find another site that supports the same genome version as the other data providers it gets data from.  Howeverand contains sequence data. However, if you are working with a newly sequenced genome or don't want to use other groups' servers, you can support IGB's sequence visualization functionality by setting up your own sequences to distribute.

To do this, you will need to obtain sequence files and convert them to one of two specialized compressed binary formats (bnib or 2bita binary format (twobit) that allow IGB to quickly obtain all or part of the sequence data when users press the Get Sequence buttons.We strongly recommend you use the UCSC Genome Bioinformatics 2bit format for distribution of sequence files. The 2bit Sequence button, run a blast search, or open the Sequence Viewer window.

The twobit format was first developed for the blat cDNA-to-genome alignment tool; . IGB 2bit uses to support efficient retrieval of sequence data. To convert a fasta format file to 2bittwobit, use a program called faToTwoBit available from http://hgdownload.cse.ucsc.edu/admin/exe/.

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Code Block
$ twoBitInfo A_thaliana_Jun_2009.2bit genome.txt

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Step Eight: Add your new QuickLoad site to IGB.
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