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    codecov[bot] commented #1125
Robin Haw
@hawrobin
And it gets crazier when that’s part of normal biology!
Colin Diesh
@cmdcolin
ya. lot of unknowns in both normal/disease biology. the point of that slide is actually that they do not know what the "toxicity" is for the gene, just that the repeat expansion causes some toxicity (that could be accumulation of those nonsense peptides or other reasons)
Colin Diesh
@cmdcolin
or, how should apollo annotate disease states in general
out.png
disease state has cryptic exon, suppressed in normal biology (should that be included in a gene set export? just something to ponder)
its a little bit of having a hammer (genome browsers/apollo) and wanting to apply it to stuff like this, but just fun to think about
Robin Haw
@hawrobin
maybe thinking a bit more about this - how does someone visualize at the gene, transcript or protein level, the changes in sequence or regions/domains that reflect the transition from normal biology to disease state?
how do you allow users to annotate this?
Colin Diesh
@cmdcolin
ya, i think the one above is cool because it nicely visualizes the cryptic splicing
but then it is some question of: how to represent that as an annotation
Colin Diesh
@cmdcolin
in gencode gff there are sometimes funny things in column 9 that says like transcript_type=nonsense_mediated_decay or tag=mRNA_end_NF (no stop codon found i presume) but that is pretty custom
Robert Buels
@rbuels
wouldn't the "diseased state" just be a variant?
but perhaps current vcf might not be able to express that weird thing
Colin Diesh
@cmdcolin
its complicated interplay of gene regulation is related to TDP43 binding to STMN2, there may not even be a variant involved
Robin Haw
@hawrobin
That’s where interaction and pathway databases come into play!
Colin Diesh
@cmdcolin
presentation from washu epigenome browser pi now
Nathan Dunn
@nathandunn
image.png
FYI, in the demo when I zoom in I get this:
image.png
Colin Diesh
@cmdcolin
@nathandunn ya that is a bug in 1.1.0...a fix is on main line pending next release
Nathan Dunn
@nathandunn
:+1:
Colin Diesh
@cmdcolin
cool example of transposon generating alternative splice form
Screenshot from 2021-04-12 15-26-37.png
(the mt2b2/l2a charlie are transposons upstream of the canonical exon1 and are active in the early embryo across different species)
Robin Haw
@hawrobin
@all there is one JBrowse GSoC project proposal. Who should I sign up as mentors?
can you please provide a gmail email address I can use to register you with?
Robert Buels
@rbuels
@hawrobin sign me up; rbuels@gmail.com
other devs are really busy
Robert Buels
@rbuels
congrats to @mattmorgan6 on first publish of @gmod/trix
1 reply
peterkxie
@peterkxie
🎉
Elliot Hershberg
@elliothershberg
Wooo
:shipit:
Awesome work!
Teresa Martinez
@teresam856
ayyyy 🥳👏👏👏👏
Robin Haw
@hawrobin
@rbuels thx, will do
Colin Diesh
@cmdcolin
nice work @mattmorgan6
might make a question to the issue forum...was trying out the example from the readme
Elliot Hershberg
@elliothershberg
What is the status of lab meeting today?
Robert Buels
@rbuels
good question, was wondering that myself
Colin Diesh
@cmdcolin
signed myself up for a lab meeting slot/lightning talk if there was still going to be one
Shihab Dider
@shihabdider
I believe I'm presenting a technical(ish) talk today.
Ian Holmes
@ihh
Hi, I neglected to ensure the lab meeting schedule doc was up to date. My bad. Can Shihab give today's talk and maybe Garrett and Colin next week?
Colin Diesh
@cmdcolin
ya no worries
Robert Buels
@rbuels
i'm gonna be slightly late for labmeeting, in a tech interview for apollo that's running a tad long
Ian Holmes
@ihh
OK
Robert Buels
@rbuels
running a tiny bit late for grooming, another apollo tech interview right before
just a couple mins
Robert Buels
@rbuels
trix-js 0.2.0 released