I noticed remote bigWig files (http URL) take sometimes about 1 minute to load on IGV. Once they loaded, jumping from one region to another can also take several seconds.
My understanding is that bigWig files have an internal index for different chunks of different sizes. Can the index be modified so that the speed of loading on IGV is improved? Does this need to happen at the point of creation of the bigWig file, or can the index of an existing bigWig be updated to speed up loading?
You would need to do this when creating the bigWig file. Note that I'm not aware of anything that allows manually setting the various zoom levels (libBigWig/pyBigWig will allow you to set a max number, but that's it).
This then raises the question of whether IGV is using an appropriate zoom level to begin with. I've never looked at how it chooses which of the zoom levels to use, but I know it uses them since if you don't have any it will fail to load bigWig files.
Honestly, though, if it's taking a minute to jump to a new region then I suspect that the network is just slow or the remote server is overtaxed. Changing the internal indexing isn't going to fix that.
