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Bio

JBrowse 2 release

GMOD News - Mon, 11/09/2020 - 18:22
JBrowse

We are pleased to announce the first public release of JBrowse 2!

JBrowse 2 is the successor to JBrowse, but is a completely new application written with modern web standards and frameworks.

Some of the features new to JBrowse 2 include:

  • New types of views, including circular, synteny, and dotplot views
  • Graphical configuration editing
  • Connections to resources such as UCSC Track Hubs

You can see some demos of JBrowse 2 in action here. To get started using JBrowse 2, visit our quickstart guide here.

We'd love to hear what you think! You can find information about how to contact us here.

The JBrowse Team

Posted to the GMOD News on 2020/11/09
Categories: Bio

News/JBrowse 2 release

GMOD.org recent changes - Mon, 11/09/2020 - 18:22

← Older revision Revision as of 23:22, 9 November 2020 Line 16: Line 16:     The JBrowse Team The JBrowse Team  +{{NewsItem|2020/11/09}} Garrett
Categories: Bio

News/JBrowse 2 release

GMOD.org recent changes - Mon, 11/09/2020 - 18:21

JBrowse 2 release

New page

[[File:jbrowse2_logo.png|200px|right|link=https://jbrowse.org/jb2/|JBrowse]]

We are pleased to announce the first public release of [https://jbrowse.org/jb2/ JBrowse 2]!

JBrowse 2 is the successor to JBrowse, but is a completely new application written with modern web standards and frameworks.

Some of the features new to JBrowse 2 include:

* New types of views, including circular, synteny, and dotplot views
* Graphical configuration editing
* Connections to resources such as UCSC Track Hubs

You can see some demos of JBrowse 2 in action [https://jbrowse.org/jb2/demos/ here]. To get started using JBrowse 2, visit our quickstart guide [https://jbrowse.org/jb2/docs/quickstart_web/ here].

We'd love to hear what you think! You can find information about how to contact us [https://jbrowse.org/jb2/contact/ here].

The JBrowse Team Garrett
Categories: Bio

File:Jbrowse2 logo.png

GMOD.org recent changes - Mon, 11/09/2020 - 18:17

Garrett uploaded "File:Jbrowse2 logo.png" JBrowse 2 logo

Garrett
Categories: Bio

JBrowse Configuration Guide

GMOD.org recent changes - Tue, 09/29/2020 - 22:48

‎Apache Configuration Note

← Older revision Revision as of 02:48, 30 September 2020 Line 1,168: Line 1,168:  If you are using the Apache web server, please be aware that the module <code>mime_magic</code> can cause BAM files to be served incorrectly.  Usually, the error in the web developer console will be something like "Not a BAM file".  Some packaged versions of Apache, particularly on Red Hat or CentOS-based systems, are configured with this module turned on by default.  We recommend you deactivate this Apache module for the server or directory used to serve JBrowse files.  If you do not want to deactivate this module for the entire server, try adding this line to your HTTPD config or .htaccess file: If you are using the Apache web server, please be aware that the module <code>mime_magic</code> can cause BAM files to be served incorrectly.  Usually, the error in the web developer console will be something like "Not a BAM file".  Some packaged versions of Apache, particularly on Red Hat or CentOS-based systems, are configured with this module turned on by default.  We recommend you deactivate this Apache module for the server or directory used to serve JBrowse files.  If you do not want to deactivate this module for the entire server, try adding this line to your HTTPD config or .htaccess file:       AddType application/octet-stream .bam .bami .bai      AddType application/octet-stream .bam .bami .bai  +  +In some cases the problem can also manifest in VCF tabix for example, you may also need to use  +  +    AddType application/octet-stream .gz  +    AddType application/octet-stream .tbi  +    AddEncoding dummy .gz .tbi  +  +Note that there may be some sideeffect related to downloading gz files from this, but it has been reported to fix jbrowse usage of tabix VCF. Let us know if you have other solutions     = Wiggle/BigWig Tracks (XYPlot, Density) = = Wiggle/BigWig Tracks (XYPlot, Density) = Colin Diesh
Categories: Bio

JBrowse FAQ

GMOD.org recent changes - Wed, 09/16/2020 - 11:23

‎What is the difference between CanvasFeatures and HTMLFeatures?

← Older revision Revision as of 15:23, 16 September 2020 Line 267: Line 267:     * CanvasFeatures are newer. * CanvasFeatures are newer. −* CanvasFeatures can support Gene glyphs, i.e., a gene with multiple transcripts are grouped together on the screen. In HTMLFeatures, you have to load at the &quot;transcript&quot; level, so this loses the gene level info (if you do try to load the --type gene, it will just load &quot;gene spans&quot;, but then it doesn't display the transcript subfeatures. not terrible, but not as cool as CanvasFeatures).+* CanvasFeatures can support Gene glyphs, i.e., a gene with multiple transcripts are grouped together on the screen. In HTMLFeatures, you have to load at the &quot;transcript&quot; level, so this loses the gene level info (if you do try to load the --type gene, it will just load &quot;gene spans&quot;, but then it doesn't display the transcript subfeatures. You have to use --type mRNA or similar with HTMLFeatures to see the transcripts!).  * CanvasFeatures are faster if your have a lot of data. * CanvasFeatures are faster if your have a lot of data. −* They can support more dynamic shapes (See the SashimiPlot plugin https://github.com/cmdcolin/sashimiplot for example of Arc track, or NeatCanvasFeatures for example of "intron hats")   * They have different configuration functions. All the "style" methods on CanvasFeatures can be callback functions, so you can have a dynamic callback for the feature color, label, etc. The "glyph" can also be a callback, so you can make a function to change to a box or diamond glyph depending on feature attributes.   * They have different configuration functions. All the "style" methods on CanvasFeatures can be callback functions, so you can have a dynamic callback for the feature color, label, etc. The "glyph" can also be a callback, so you can make a function to change to a box or diamond glyph depending on feature attributes.    * CanvasFeatures have better mouseovers. The HTMLFeatures mouseovers use the HTML title attribute which can only display plain text. On CanvasFeatures tracks, the mouseover it is a real tooltip that you can embed arbitrary HTML inside of. * CanvasFeatures have better mouseovers. The HTMLFeatures mouseovers use the HTML title attribute which can only display plain text. On CanvasFeatures tracks, the mouseover it is a real tooltip that you can embed arbitrary HTML inside of. Colin Diesh
Categories: Bio

AGR GFF

AGR GFF uploads - Wed, 08/19/2020 - 04:35
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Categories: Bio