Pull Fastas based on two annotations and assess

sr320 commented 1 year ago

Assess quality of annotation by determining completion of gene set.

sr320 commented 1 year ago

@laurahspencer can you provide the two annotation files?

laurahspencer commented 1 year ago

GAWN (Genome Annotation Without Nightmares):

Following the GAWN instructions I ran the script GAWN-annotation.sh using the scaffold-only genome, the transcriptome that Giles generated for me, the Swissprot database, and the config file gawn_config.sh. All resulting files are on Google Drive here, but the files <100MB are also in this repo here. Feel free to drop any files resulting from your work in either location.

GenSaS:

All resulting files are on Google Drive here, and files <100 MB are also in this repo here (which includes all except for the repeat elements).
If anyone has a GenSaS account I can share the project with you, I just need to know your username.
Note that GenSaS was run with the full genome, so any resulting files should be filtered for only the scaffolds.

kubu4 commented 1 year ago

I'll take a GenSas share!

User: kubu4

Thanks!

laurahspencer commented 1 year ago

@kubu4 just added you!

sr320 commented 1 year ago

I say we go with GenSas annotation - needs to be trimmed up a bit to remove unscaffolded - did that (and more) here

laurahspencer / DuMOAR