(Michael Lawrence)
I think I have mentioned to you before that it would be nice to have the arcs drawn on the alignment track, rather than the gene track, because we'll often have multiple BAM datasets. They won't all fit on the gene track.

(Michael Lawrence)
Here is a screenshot of what we're doing in R for transcript isoforms. It's not perfect, but it shows the general idea. Have a gene track, and then for each BAM, we show the coverage, along with the arcs, with the thickness mapped from the number of reads crossing the junction.

Here are some possible interactive features:

• User selects a transcript, we somehow highlight/overlay the coverage and arcs that are compatible with that transcript. Optionally, we could limit the coverage/arcs to the reads that are uniquely mapped (in a compatible way) to that transcript. The same thing goes for selecting an exon, or an intron (representing the junction).

• User selects an arc, we highlight/overlay the coverage/arcs for the selected reads. Also, we highlight the transcripts that have that junction.

also:
on A. thal current genome. Load a bam (this might be a problem on human too - so feel free to try it there)

Activate trans.iso. plug-in. Select reference tier, generate chevrons. Click a chevron, notice reads are highlighted. Click another chevron, the next set of reads is highlighted - but the first group is never DEselected.