Difference between revisions of "Integration"
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Start as it has better cross-platform and cross-browser support. | Start as it has better cross-platform and cross-browser support. | ||
| − | + | ==General considerations== | |
| + | To present your data in GenomeView optimally, there are a number of things you have to keep in mind. | ||
| + | |||
| + | |||
| + | ===Indexing=== | ||
| + | Please follow the recommendation in the [[recommended file formats]] page. | ||
| + | |||
| + | You will want to <a href="/content/preparing-fasta-files">index your reference sequence</a> to reduce loading times. | ||
| + | |||
| + | You may want to index annotation files, but this is not recommended unless they are over 10 Mb when compressed with gzip because you will loose structural information. | ||
| + | |||
| + | <p>To load an indexed file, you point GenomeView to the main file and GenomeView will try to find the index by itself. | ||
| + | |||
| + | |||
| + | ===Compression=== | ||
| + | <p>GenomeView supports GZIP compression transparently on all non-indexed file formats, i.e. compression and indexing are mutually exclusive. However as part of the indexing process, many file formats will be compressed. | ||
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| + | |||
| + | |||
| + | <p><strong>Short read data</strong> | ||
| + | <p>Depending on what information you want to get out of the visualization, there are basically two ways to load short read data. The first one is the <a href="/content/short-read-track">Short Read Track</a> which will give you a detailed view with all individual reads. The second one is the <a href="/content/pile-track">Pile up track</a> which will give a more of a summary view/ coverage plot based on your sequence reads. | ||
| + | |||
| + | <p><a href="/content/preparing-short-read-alignments">Instructions to prepare data for the short read track</a> | ||
| + | |||
| + | <p><a href="/content/preparing-pileup">Instructions to prepare data for the pile up track</a> | ||
Very nice site! | Very nice site! | ||
Revision as of 17:08, 3 June 2014
http://genomeview.org/content/integration
Other topics that may be of interest: <a href="/content/integrating-genomeview-editor">Integrating as editor</a> and <a href="/content/communicating-genomeview">Communicating with GenomeView</a>
This page tries to explain how to integrate GenomeView in your website with your data. You can either make it available through Java Webstart, or as an applet. Whenever possible we recommend using Java Web Start as it has better cross-platform and cross-browser support.
General considerations
To present your data in GenomeView optimally, there are a number of things you have to keep in mind.
Indexing
Please follow the recommendation in the recommended file formats page.
You will want to <a href="/content/preparing-fasta-files">index your reference sequence</a> to reduce loading times.
You may want to index annotation files, but this is not recommended unless they are over 10 Mb when compressed with gzip because you will loose structural information.
To load an indexed file, you point GenomeView to the main file and GenomeView will try to find the index by itself.
Compression
GenomeView supports GZIP compression transparently on all non-indexed file formats, i.e. compression and indexing are mutually exclusive. However as part of the indexing process, many file formats will be compressed.
Short read data
Depending on what information you want to get out of the visualization, there are basically two ways to load short read data. The first one is the <a href="/content/short-read-track">Short Read Track</a> which will give you a detailed view with all individual reads. The second one is the <a href="/content/pile-track">Pile up track</a> which will give a more of a summary view/ coverage plot based on your sequence reads.
<a href="/content/preparing-short-read-alignments">Instructions to prepare data for the short read track</a>
<a href="/content/preparing-pileup">Instructions to prepare data for the pile up track</a> Very nice site! Very nice site! Very nice site!