Next-gen sequencing applications go after beyond genome sequencing. So I am wondering if the current genome browsers are sufficient for visualizing RNA-seq data? Else what you use to visualize RNA-seq data?
In my experience, RNA-seq data on genome tracks can help visualize spatial relationships between expression and other genome annotations, but does a poor job of visualizing change in expression over conditions and quantifying the results.
I have been working on genome/transcriptome browser for visualizing RNA-seq results. tbrowse offers the familiar genome track visualization, but also quantitates and plots expression over samples.
Also tbrowse is a HTML5/JavaScript/ajax based application designed to completely segregate data from visualization. All the visualizations are rendered using HTML5 and javascript and the required data is requested through ajax. This makes development much easier, reduces the load on servers and offeres a much more interactive experience to users.
This framework is designed to be easily extended to include other types of visualizations, such as SNPs, CNVs and alternative splicing.
There is a demo at http://butler.fri.uni-lj.si/anup/tbrowse/
tutorial: http://butler.fri.uni-lj.si/anup/tbr...e_tutorial.swf
The code and documentation are at http://code.google.com/p/tbrowse/
Anup Parikh
In my experience, RNA-seq data on genome tracks can help visualize spatial relationships between expression and other genome annotations, but does a poor job of visualizing change in expression over conditions and quantifying the results.
I have been working on genome/transcriptome browser for visualizing RNA-seq results. tbrowse offers the familiar genome track visualization, but also quantitates and plots expression over samples.
Also tbrowse is a HTML5/JavaScript/ajax based application designed to completely segregate data from visualization. All the visualizations are rendered using HTML5 and javascript and the required data is requested through ajax. This makes development much easier, reduces the load on servers and offeres a much more interactive experience to users.
This framework is designed to be easily extended to include other types of visualizations, such as SNPs, CNVs and alternative splicing.
There is a demo at http://butler.fri.uni-lj.si/anup/tbrowse/
tutorial: http://butler.fri.uni-lj.si/anup/tbr...e_tutorial.swf
The code and documentation are at http://code.google.com/p/tbrowse/
Anup Parikh