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genomeannotation / GAG

Generates an NCBI .tbl file of annotations on a genome.
MIT License
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Impact of fixing start and stop codons #162

Closed tarunaaggarwal closed 9 years ago

tarunaaggarwal commented 9 years ago

Hi. I used the fix_start_stop flag on an annotated genome; however, after fixing the codons, none of the other metrics changed? I was wondering if you can please explain why that is? Thanks!

nextgenusfs commented 9 years ago

Hi @tarunaaggarwal - I believe that the fix_start_stop codons is just annotating the start and stop in your GFF output, so it doesn't filter out gene models that don't have appropriate start and stops. @bruab will need to confirm.

bruab commented 9 years ago

Hi @tarunaaggarwal! What @nextgenusfs says is correct -- all the --fix_start_stop option does is inspect CDS boundaries and create start/stop codon features where appropriate. Are you looking to do something more elaborate?

tarunaaggarwal commented 9 years ago

No not necessarily. It was just worrisome when after fixing the start and stop codons, none of the other metrics changed since they depend on where these codons are. For instance, shouldn't the CDS total length change if start and stop codons shift?

nextgenusfs commented 9 years ago

Perhaps the name (--fix_start_stop) is throwing you off - it is only annotating start and stop codons and is thus not changing your gene models at all, so the metrics shouldn't change.

tarunaaggarwal commented 9 years ago

Oh I see. Alright. Well, thanks a bunch for your help and explanation!

bruab commented 9 years ago

@nextgenusfs Thanks!