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Arcadia-Science / 2023-amblyomma-americanum-txome-assembly

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Add code to predict open reading frames #11

Closed taylorreiter closed 11 months ago

taylorreiter commented 11 months ago

I may eventually swap this out for dammit annotation, but I think this is good enough for now.

dammit runs transdecoder, a bunch of functional annotation tools, and wraps everything in a gff file. i expect dammit will take some time to run bc functional annotation is expensive. it has an option to keep the same contig names, so I can play with that for consistency as well.

~#5 and #9 should be reviewed before this one.~ done

This may end up getting ripped out in favor of dammit annotation (see #13), which wraps transdecoder, but at least it's recorded here for now, and it will stay in if dammit ends up being buggy.

taylorreiter commented 11 months ago

@ecpierce -- want to compare notes with @elizabethmcd to see if you ran into the same problems with transdecoder?

ecpierce commented 11 months ago

Yes! My problem only seemed to be the need to add the 'no refine starts' flag when there are too few transcripts (https://github.com/Arcadia-Science/2023-chelicerate-analysis/issues/16). Maybe that is what you encountered too @elizabethmcd ?