search

GMOD / jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
http://jbrowse.org
Other
460 stars 199 forks source link

Generate spliced mRNA sequence in "Gene details view" #633

Closed billzt closed 8 years ago

billzt commented 8 years ago

Suppose a gene with exon-intron structures like this: a

If you click on this gene, you can view and download the genomic sequence, "mRNA sequence" and each exon sequence in a "gene details view" pop-up window. In this situation, the viewed "mRNA sequence" is unspliced. In fact, it is exactly the same with genomic sequence. If users want to obtain the spliced mRNA sequences, the only method is to manually connect exons one by one, which seems inconvenience.

I'll be very glad if we can obtain spliced mRNA sequence automatically in the "Gene details view"!

colindaven commented 8 years ago

You can use a JBrowse plugin for this: https://github.com/tsaari88/FeatureSequence

billzt commented 8 years ago

Yes, this could be deal with https://github.com/tsaari88/FeatureSequence