[maker-devel] cds error

[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-devel-bounces at yandell-lab.org> On Behalf Of Jacques Dainat
Sent: 18 December 2021 10:13
To: zc y <prometheus07.06 at gmail.com>
Cc: maker-devel at 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.

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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FNBISweden%2FAGAT%2Fblob%2Fmaster%2Fbin%2Fagat_sp_extract_sequences.pl&data=04%7C01%7Crobert.king%40rothamsted.ac.uk%7Cd70594edd7b44001bbac08d9c20f0b9d%7Cb688362589414342b0e37b8cc8392f64%7C1%7C0%7C637754192142883927%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=A6HCJ%2FVL%2F2tLTf2%2BEJ6Q3rA%2FX9nOPoSyU0og5RMk5B0%3D&reserved=0> from AGAT (https://github.com/NBISweden/AGAT<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FNBISweden%2FAGAT&data=04%7C01%7Crobert.king%40rothamsted.ac.uk%7Cd70594edd7b44001bbac08d9c20f0b9d%7Cb688362589414342b0e37b8cc8392f64%7C1%7C0%7C637754192142893882%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=SYDdYM%2BMWAY11RKjyJ%2Fqt4vlB5%2BBjCvPpVQ6nGU6a8U%3D&reserved=0>) 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<mailto: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>
_______________________________________________
maker-devel mailing list
maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org


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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20220112/949c737f/attachment-0002.html>