Make a new displayMode that collapsed transcript isoforms

[cmdcolin]

In many cases, the large number of transcript isoforms is a bit overwhelming. The reducedRepresentation displayMode is nice but it just draws a block instead of any exon-intron structure

A nice reference point for this could be the biodalliance default gene track https://www.biodalliance.org/

Clicking the plus icon on the track label expands out the transcript isoforms

[cmdcolin]

Some discussion on gmod-ajax here, jb1 related but probably related to jb2 also https://sourceforge.net/p/gmod/mailman/message/37348867/

[cmdcolin]

another option, which would not mash up the data as bad, would be to display something like just the "MANE select" transcript

the context of this problem is that, in many cases, rendering every single transcript isoform is too much detail, you just want the basic notion of what the gene structure is.

options

• "collapsing all isoforms" into a single glyph is a bit of a misrepresentation of the gene model
• displaying one transcript isoform randomly could choose potentially not a very representative one
• choosing MANE select e.g. https://www.ncbi.nlm.nih.gov/refseq/MANE/ would make sure the choice was at least a fairly good choice

MANE select transcripts have "tag=MANE select" in the GFF3 column 9

[cmdcolin]

note that not all transcripts have a MANE select transcript, e.g. some lncRNAs

[cmdcolin]

might just be that MANE transcripts is a separate track rather than a display mode that is toggled