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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">If change second from last column to just . then that usually fixes this kind of problem or try script indicated.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">Gffread with x parameter and not w right..<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> maker-devel <maker-devel-bounces@yandell-lab.org>
<b>On Behalf Of </b>Jacques Dainat<br>
<b>Sent:</b> 18 December 2021 10:13<br>
<b>To:</b> zc y <prometheus07.06@gmail.com><br>
<b>Cc:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> Re: [maker-devel] cds error<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="line-height:12.0pt;background:#FFEB9C"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#9C6500">CAUTION:</span><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:black"> 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.<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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 <a href="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" title="agat_sp_extract_sequences.pl"><span style="font-size:10.5pt;font-family:"Segoe UI",sans-serif;text-decoration:none">agat_sp_extract_sequences.pl</span></a> from AGAT
(<a href="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">https://github.com/NBISweden/AGAT</a>)
is dealing properly with incomplete CDS and first codon with offset. You might give a try to see if it fix the issue. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best regards, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:black">Jacques Dainat, Ph.D.<o:p></o:p></span></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal">On 29 Nov 2021, at 05:20, zc y <<a href="mailto:prometheus07.06@gmail.com">prometheus07.06@gmail.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Dear Maker developers, <o:p></o:p></p>
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<p class="MsoNormal">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. <o:p></o:p></p>
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<p class="MsoNormal">In fact, I checked the protein file (Chr12.maker.proteins.fasta) provided by the maker, it is correct. <o:p></o:p></p>
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<p class="MsoNormal">I used the same parameter and evidence in another rice, it don't have the problem.<o:p></o:p></p>
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<p class="MsoNormal">What should I do?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">thanks,<o:p></o:p></p>
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<p class="MsoNormal"><QQ<span lang="ZH-CN">截图</span>20211129121755.png><QQ<span lang="ZH-CN">截图</span>20211129121917.png><o:p></o:p></p>
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<p class="MsoNormal">_______________________________________________<br>
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<p class="MsoNormal"><o:p> </o:p></p>
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