Difference between revisions of "Track (element type)"

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(Created page with "{{Element type|track|ru.biosoft.bsa.Track}} {{Stub|pictures and more detailed track types information}} === Description === '''Track''' is an element which contains genomic fe...")
 
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{{Stub|pictures and more detailed track types information}}
 
{{Stub|pictures and more detailed track types information}}
 
=== Description ===
 
=== Description ===
'''Track''' is an element which contains genomic features (or '''sites'''). There are various implementations of tracks which provide the unified track interface for different sources including Ensembl database, SQL database for user uploaded data, BAM files, remote DAS servers and so on.
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'''Track''' is an element which contains genomic features (or '''sites'''). There are various implementations of tracks which provide the unified track interface for different sources including the Ensembl database, SQL database for user uploaded data, BAM files, remote DAS servers and so on.
  
The main function of the track is to provide list of sites located in specified region of the specified {{Type link|sequence}}. Each site has genomic coordinates, strand and a number of annotation fields. Also every track has a '''TrackViewBuilder''' associated with it, which controls how these sites will be drawn in the [[genome browser]]. Thanks to this different tracks are displayed in different ways.
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The main function of the track is to provide a list of sites located in a specified region of a specified {{Type link|sequence}}. Each site has genomic coordinates, strand and a number of annotation fields. Also every track has a '''TrackViewBuilder''' associated with it, which controls how these sites will be drawn in the [[genome browser]]. Thanks to this, different tracks are displayed in different ways.
  
 
Most of the tracks are associated with some sequences collection. In this case you can double click on the track to open it in the [[genome browser]]. Alternatively you can first open the {{Type link|sequence}} in the genome browser, then drag the track on it to add it to the view.
 
Most of the tracks are associated with some sequences collection. In this case you can double click on the track to open it in the [[genome browser]]. Alternatively you can first open the {{Type link|sequence}} in the genome browser, then drag the track on it to add it to the view.
  
Some tracks can be opened as [[table document]] using [[File:WebAction-tree-open_table-icon.png]] '''Open as table''' context action. In this case list of all sites in the track will be displayed in tabular form with the ability to sort, filter and so on.
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Some tracks can be opened as a [[table document]] using the [[File:WebAction-tree-open_table-icon.png]] '''Open as table''' context action. In this case a list of all sites in the track will be displayed in tabular form with the ability to sort, filter and so on.
  
Some tracks also work as collections of sequences. Every sequence in this collection corresponds to the track site. These sequences can be opened in genome browser as well.
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Some tracks also work as collections of sequences. Every sequence in this collection corresponds to a track site. These sequences can be opened in the genome browser as well.
  
 
Tracks can be imported from many different file formats including [[SAM or BAM alignment file|BAM]], [[BED format|BED]], [[General Feature Format|GFF]], [[VCF format|VCF]] and many more. Tracks are used and produced by numerous analysis methods.
 
Tracks can be imported from many different file formats including [[SAM or BAM alignment file|BAM]], [[BED format|BED]], [[General Feature Format|GFF]], [[VCF format|VCF]] and many more. Tracks are used and produced by numerous analysis methods.
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==See also==
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*[[Genome browser]]
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*[[Ensembl]]

Latest revision as of 13:29, 27 June 2013

Title
Type-track-icon.png track
Class
Track
This page or section is a stub. Please add pictures and more detailed track types information here!

[edit] Description

Track is an element which contains genomic features (or sites). There are various implementations of tracks which provide the unified track interface for different sources including the Ensembl database, SQL database for user uploaded data, BAM files, remote DAS servers and so on.

The main function of the track is to provide a list of sites located in a specified region of a specified Type-sequence-icon.png sequence. Each site has genomic coordinates, strand and a number of annotation fields. Also every track has a TrackViewBuilder associated with it, which controls how these sites will be drawn in the genome browser. Thanks to this, different tracks are displayed in different ways.

Most of the tracks are associated with some sequences collection. In this case you can double click on the track to open it in the genome browser. Alternatively you can first open the Type-sequence-icon.png sequence in the genome browser, then drag the track on it to add it to the view.

Some tracks can be opened as a table document using the WebAction-tree-open table-icon.png Open as table context action. In this case a list of all sites in the track will be displayed in tabular form with the ability to sort, filter and so on.

Some tracks also work as collections of sequences. Every sequence in this collection corresponds to a track site. These sequences can be opened in the genome browser as well.

Tracks can be imported from many different file formats including BAM, BED, GFF, VCF and many more. Tracks are used and produced by numerous analysis methods.

[edit] See also

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