cds:incomplete warning

[Brent-Saylor-Canopy]

Hi, I'm using snap to generate gene models for a maker annotation of a new plant species. So far Snap has been great to work with.

My question comes in when selecting the gene models to use for SNAP. So far I have been taking models from Maker, running CDhit to filter out highly similar sequences, then using that to train the next round of snap. I'm not getting any errors when I validate my zff files, but I see a lot of the cds: incomplete and intron/exon short warnings. What should I be looking for as far as validating these in a browser, and would it be problematic to leave out everything this this type of warning for the next training round?

Thanks for any help you can provide,

[iankorf]

You get incomplete genes at the ends of sequences. If you have a lot of "chromosomes" you will get lots of incomplete genes. These won't be used for training, and will end up in the warning pile. It's safe to ignore these.

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On Sep 23, 2022, at 8:13 AM, Brent-Saylor-Canopy ***@***.***> wrote: Hi, I'm using snap to generate gene models for a maker annotation of a new plant species. So far Snap has been great to work with. My question comes in when selecting the gene models to use for SNAP. So far I have been taking models from Maker, running CDhit to filter out highly similar sequences, then using that to train the next round of snap. I'm not getting any errors when I validate my zff files, but I see a lot of the cds: incomplete and intron/exon short warnings. What should I be looking for as far as validating these in a browser, and would it be problematic to leave out everything this this type of warning for the next training round? Thanks for any help you can provide, — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.