[maker-devel] cds error

[Jacques Dainat]

Hi,

Might be related to fragmented CDS where the beginning is missing. The offset (phase) might be different than 0. It is 0 when there is the complete start codon. I don’t know how deals gffread with the offset. You can check within the GFF file if the incriminated genes have this kind of CDS offset start. I know that  agat_sp_extract_sequences.pl <https://github.com/NBISweden/AGAT/blob/master/bin/agat_sp_extract_sequences.pl> from AGAT (https://github.com/NBISweden/AGAT) is dealing properly with incomplete CDS and first codon with offset. You might give a try to see if it fix the issue. 

Best regards, 

Jacques Dainat, Ph.D.


> On 29 Nov 2021, at 05:20, zc y <prometheus07.06 at gmail.com> wrote:
> 
> Dear  Maker developers,
> I found a CDS error in my rice project. I ran the maker (3.01.03) and it finished without error in master_datastore_index.log. But when I use gffread to translate the protein from maker gff, I found that almost all of proteins are not start with 'M' and many stop codons in it. 
> In fact, I checked the protein file (Chr12.maker.proteins.fasta) provided by the maker, it is correct. 
> I used the same parameter and evidence in another rice, it don't have the problem.
> What should I do?
> 
> 
> thanks,
> <QQ截图20211129121755.png><QQ截图20211129121917.png>
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