comparison jbrowse2.xml @ 5:efc64d8f4b72 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9

4:54396f0323f4

**Track Groups** represent a set of tracks in a single category. These
can be used to let your users understand relationships between large
groups of tracks.

.. image:: sections.png

Annotation Tracks
-----------------

There are a few different types of tracks supported, each with their own
set of options:

~~~~~~~~

These are standard feature tracks. They usually highlight genes,
mRNAs and other features of interest along a genomic region.

BAM Pileups
~~~~~~~~~~~

We support BAM files and can automatically generate SNP tracks based on
that bam data.


BlastXML
~~~~~~~~

.. image:: blast.png

JiG now supports both blastn and blastp datasets. JiG internally uses a
blastXML to gapped GFF3 tool to convert your blastxml datasets into a
format amenable to visualization in JBrowse. This tool is also
available separately from the IUC on the toolshed.

10 hits or so.

**Protein blast search** option merely informs underlying tools that
they should adjust feature locations by 3x.

Bigwig XY
~~~~~~~~~

.. image:: bigwig.png



VCFs/SNPs
~~~~~~~~~

These tracks do not support any special configuration.

5:efc64d8f4b72

**Track Groups** represent a set of tracks in a single category. These
can be used to let your users understand relationships between large
groups of tracks.

Annotation Tracks
-----------------

There are a few different types of tracks supported, each with their own
set of options:

~~~~~~~~

These are standard feature tracks. They usually highlight genes,
mRNAs and other features of interest along a genomic region.

When these contain tens of millions of features, such as repeat regions from a VGP assembly, displaying one at a time leads
to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is
selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works
well for relatively sparse bed files.

BAM Pileups
~~~~~~~~~~~

We support BAM files and can automatically generate SNP tracks based on
that bam data.


BlastXML
~~~~~~~~

JiG now supports both blastn and blastp datasets. JiG internally uses a
blastXML to gapped GFF3 tool to convert your blastxml datasets into a
format amenable to visualization in JBrowse. This tool is also
available separately from the IUC on the toolshed.

10 hits or so.

**Protein blast search** option merely informs underlying tools that
they should adjust feature locations by 3x.


VCFs/SNPs
~~~~~~~~~

These tracks do not support any special configuration.