<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p.msonormal0, li.msonormal0, div.msonormal0
{mso-style-name:msonormal;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal">It looks like the adapter is primarily at the ends, which is easy to remove. However, I agree, removing these and redoing the assembly may improve the assembly quality.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">chris<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="margin-left:.5in"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">maker-devel <maker-devel-bounces@yandell-lab.org> on behalf of Xabier Vázquez-Campos <xvazquezc@gmail.com><br>
<b>Date: </b>Monday, October 23, 2017 at 5:03 PM<br>
<b>To: </b>Emmanuel Nnadi <eennadi@gmail.com><br>
<b>Cc: </b>Maker Mailing List <maker-devel@yandell-lab.org>, "Ence, daniel" <d.ence@ufl.edu><br>
<b>Subject: </b>Re: [maker-devel] Contamination report from NCBI<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><a name="_MailOriginalBody">Hi there,<o:p></o:p></a></p>
</div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody">Did you perform quality and adapter trimming of your raw reads? That's actually an assembly issue.<o:p></o:p></span></p>
</div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody">I would seriously encourage you to redo the assembly before continuing.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in">
<span style="mso-bookmark:_MailOriginalBody">If that isnt possible, start by removing those sequences and split the contigs at those places as suggested in the report.<br>
<br>
For the annotation part, not 100% sure but I'd say start with the "Merge/resolve legacy annotations" steps but maybe Carson or Daniel have a different suggestion<br>
</span><a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Merge.2FResolve_Legacy_Annotations"><span style="mso-bookmark:_MailOriginalBody">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Merge.2FResolve_Legacy_Annotations</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></p>
</div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody">Cheers,<o:p></o:p></span></p>
</div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody">Xabi<o:p></o:p></span></p>
<div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
</div>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody">On 24 October 2017 at 00:30, Emmanuel Nnadi <</span><a href="mailto:eennadi@gmail.com" target="_blank"><span style="mso-bookmark:_MailOriginalBody">eennadi@gmail.com</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody">>
wrote:<o:p></o:p></span></p>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody">Hello<o:p></o:p></span></p>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody">Good day.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody">Please I submitted my sequence to NCBI and they sent back this contamination report.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody">Please how do I use maker to effect the correction<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody">Nnadi Nnaemeka Emmanuel
<o:p></o:p></span></p>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody">Department of Microbiology,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody">Faculty of Natural and Applied Science,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody">Plateau State University, Bokkos, Plateau State, Nigeria.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody">Publications: </span><a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank"><span style="mso-bookmark:_MailOriginalBody">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></p>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in">
<span style="mso-bookmark:_MailOriginalBody"><br>
_______________________________________________<br>
maker-devel mailing list<br>
</span><a href="mailto:maker-devel@box290.bluehost.com"><span style="mso-bookmark:_MailOriginalBody">maker-devel@box290.bluehost.com</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><br>
</span><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank"><span style="mso-bookmark:_MailOriginalBody">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></p>
</blockquote>
</div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody"><br>
<br clear="all">
<br>
-- <o:p></o:p></span></p>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="mso-bookmark:_MailOriginalBody">Xabier Vázquez-Campos,
<i>PhD</i><br>
<i>Research Associate</i><br>
NSW Systems Biology Initiative<br>
School of Biotechnology and Biomolecular Sciences<br>
The University of New South Wales<br>
Sydney NSW 2052 AUSTRALIA<o:p></o:p></span></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</body>
</html>