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twsaari / FeatureSequence

JBrowse plugin to view the sequence of features
GNU General Public License v3.0
7 stars 3 forks source link

Suggestions for large transcripts? #10

Open scottcain opened 7 years ago

scottcain commented 7 years ago

Hi Travis,

I continue to love this plugin. While it works great for C. elegans at WormBase, where genes are relatively short, do you have any suggestions for working with mammals, where genes are frequently over 1 Mb. On my (admittedly aged laptop), the dialog takes a long time to show up and is has pretty poor responsiveness when it does (highlighting and scrolling are both really slow). Is this just something that users will have to deal with, or can you think of a solution?

Thanks, Scott

scottcain commented 7 years ago

If you'd like to take a look, I have a jbrowse instance with the rat genome here:

http://jbrowse.alliancegenome.org/jbrowse/?data=data%2FRattus%20norvegicus&loc=Chr1%3A137294001..139216000&tracks=All%20Genes&highlight=

twsaari commented 7 years ago

Hi Scott, unfortunately I'm currently traveling outside the country and don't have a computer to view your example. If you're getting the warning message when opening the plugin, then that means the nucleotides are being loaded individually. I created a solution for this some months ago that loads groups of nucleotides and is much faster, but it requires them to be broken into distinct non-overlapping regions. If I'm on the right path here, then there is already a solution coded and you would just have to get it to work in your use case. I'll be back in the states in a few days, so it will be easier for me to help at that point.