[maker-devel] cds error

[zc y]

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,

[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 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 <prometh...@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>

_______________________________________________
maker-devel mailing list
maker...@yandell-lab.org
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

[Robert King]

If change second from last column to just . then that usually fixes this kind of problem or try script indicated.

 

Gffread with x parameter and not w right..

 

From: maker-devel <maker-dev...@yandell-lab.org> On Behalf Of Jacques Dainat
Sent: 18 December 2021 10:13
To: zc y <prometh...@gmail.com>
Cc: maker...@yandell-lab.org
Subject: Re: [maker-devel] cds error

 

CAUTION: This email originated from outside of the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe.

Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038.