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pombase / pombase-chado

PomBase code for accessing Chado
MIT License
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Overlaps between 5'UTRs in the same conditions #1024

Open ValWood opened 1 year ago

ValWood commented 1 year ago

when we discussed https://github.com/pombase/pombase-chado/issues/1019

we talked about reporting the changes in 5' UTR overlaps in the publication (I need to check what has been published on this).

So we would need to know the difference in 5'UTR overlap between the old and the new dataset.

(I said I would open a ticket, but I forgot)

ValWood commented 1 year ago

after https://github.com/pombase/pombase-chado/issues/1019

ValWood commented 1 year ago

https://github.com/pombase/pombase-chado/issues/1049#issuecomment-1350428878 might be useful here.

would also be useful to know lengths of overlaps before/after

kimrutherford commented 1 year ago

https://github.com/pombase/pombase-chado/issues/1049#issuecomment-1350428878 might be useful here.

It's tricky because the old UTRs are no longer in Chado, so can't be queried with SQL. This will probably need a bit of Perl (or Python)

kimrutherford commented 1 year ago

Is this something we should look at soon?

ValWood commented 1 year ago

Not really. It might be interesting to report this in the genome submission paper UTR section. If you could do it sometime in the next 6 months (we will submit the genome shortly, but this is probably the last paper in the queue of 3).

kimrutherford commented 11 months ago

If you could do it sometime in the next 6 months

Time's nearly up. :-)

ValWood commented 11 months ago

Deprioritised we now have 2 other papers to submit before the genome update ;)

ValWood commented 11 months ago

We need to disambiguate the for_pub labels ;)