I have a validated GFF3 with an embedded fasta. I want to be able to browse this new annotation by scaffold. Currently I have been using APOLLO and chopping out the scaffolds I need to look at (gene hunting). I find this to be tedious and annoying.
People have mentioned that IGV can take a whole genome GFF3 Other thread. When I have tried to index the GFF3 with IGV it sucks up all my ram and I have to abort. I can play DOOM3 on my macbook, but browsing a genome is too much to ask for?
As I understand it, IGV will allow you to create your own local server configuration to load data from, but I don't know if that will help much with this issue (or if this suggestion is any different from what you are already doing). I think you should strongly consider trying GBrowse/JBrowse or a related "generic" browser, even if you are working with the human genome. GBrowse is very flexible, you can create your own annotations and display just about anything you want, regardless of the species. This will give you the ability to store your genome in relational database which will mostly solve this memory issue. If you are trying to display dense quantitative data or trying to view megabases at a time, you will run into problems with any browser in my experience. That being said, there are a lot of performance tricks you can implement with GBrowse if you have the need for it.
I have started creating a database for GBrowse. This just all seems like a lot of work for a simple task. It is also pretty far off the beaten path for me. It boggles my mind that a computer can render a 3D game no problem, but displaying rectangles kills it.
You are correct in that it is a lot of work for a simple task, but it is the most general solution that I am aware of. For the second part, I think it might depend on what you are trying to display in the rectangle, and that may require a lot of CPU and memory, whereas rendering 3D images involves processes (geometry shading, pixel processing, etc.) that can be done in parallel on GPUs.
I have started creating a database for GBrowse. This just all seems like a lot of work for a simple task. It is also pretty far off the beaten path for me. It boggles my mind that a computer can render a 3D game no problem, but displaying rectangles kills it.
You are correct in that it is a lot of work for a simple task, but it is the most general solution that I am aware of. For the second part, I think it might depend on what you are trying to display in the rectangle, and that may require a lot of CPU and memory, whereas rendering 3D images involves processes (geometry shading, pixel processing, etc.) that can be done in parallel on GPUs.