<html 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="Title" content="">
<meta name="Keywords" content="">
<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:12.0pt;
font-family:"Times New Roman";}
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
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:12.0pt;
font-family:"Times New Roman";}
span.gmailmsg
{mso-style-name:gmail_msg;}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:Calibri;
color:windowtext;}
span.msoIns
{mso-style-type:export-only;
mso-style-name:"";
text-decoration:underline;
color:teal;}
.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>
</head>
<body bgcolor="white" lang="EN-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">You can use RSEM for some initial filtering:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><a href="https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification#filtering-transcripts">https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification#filtering-transcripts</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">Then I generally use the Trinity QA steps, in particular TransRate or DETONATE:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><a href="https://github.com/trinityrnaseq/trinityrnaseq/wiki/Transcriptome-Assembly-Quality-Assessment">https://github.com/trinityrnaseq/trinityrnaseq/wiki/Transcriptome-Assembly-Quality-Assessment</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">chris<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-family:Calibri;color:black">From: </span>
</b><span style="font-family:Calibri;color:black">Salim Bougouffa <mjfi2sb3@gmail.com><br>
<b>Date: </b>Tuesday, January 31, 2017 at 3:14 PM<br>
<b>To: </b>Chris Fields <cjfields@illinois.edu>, Scott Cain <scott@scottcain.net>, Maya Britstein <mayabritstein@gmail.com><br>
<b>Cc: </b>"maker-devel@yandell-lab.org List" <maker-devel@yandell-lab.org>, "help@gmod.org" <help@gmod.org><br>
<b>Subject: </b>Re: [maker-devel] GFF3 file format<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p>Hi Christopher,<o:p></o:p></p>
<p>How would you identify a low confidence transcript? And how do you remove them? Also, did you try setting a minimum read coverage in Trinity as the default is one?
<o:p></o:p></p>
<p>Best<br>
/SB<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">On Thu, 26 Jan 2017, 01:04 Fields, Christopher J, <<a href="mailto:cjfields@illinois.edu">cjfields@illinois.edu</a>> wrote:<o:p></o:p></p>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">If I recall, from a BAM you would need to run a reference-based assembly on these data (e.g. Cufflinks2 or StringTie) to get this; you can also use Trinity for ref-based assembly.
But I always choose the route of a full de novo assembly (again, Trinity or similar) when possible, doing some basic cleanup (e.g. remove low confidence transcripts) and bring them as EST evidence. <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">chris <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
</div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><span class="gmailmsg"><b><span style="font-family:Calibri;color:black">From:
</span></b></span><span style="font-family:Calibri;color:black">maker-devel <<a href="mailto:maker-devel-bounces@yandell-lab.org" target="_blank">maker-devel-bounces@yandell-lab.org</a>> on behalf of Scott Cain <<a href="mailto:scott@scottcain.net" target="_blank">scott@scottcain.net</a>><br>
<span class="gmailmsg"><b>Date: </b></span>Wednesday, January 25, 2017 at 2:23 PM<br>
<span class="gmailmsg"><b>To: </b></span>Maya Britstein <<a href="mailto:mayabritstein@gmail.com" target="_blank">mayabritstein@gmail.com</a>><br>
<span class="gmailmsg"><b>Cc: </b></span>"<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a> List" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>>, "<a href="mailto:help@gmod.org" target="_blank">help@gmod.org</a>"
<<a href="mailto:help@gmod.org" target="_blank">help@gmod.org</a>><br>
<span class="gmailmsg"><b>Subject: </b></span>Re: [maker-devel] GFF3 file format<o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
</div>
<blockquote style="border:none;border-left:solid #B5C4DF 4.5pt;padding:0in 0in 0in 4.0pt;margin-left:3.75pt;margin-right:0in" id="m_-1351972388141770776MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE">
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">Hi Maya,
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">I'm not sure what MAKER's requirements are in this regard--I'm forwarding this to their mailing list.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">Scott<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">On Wed, Jan 25, 2017 at 3:12 PM, Maya Britstein
<span class="gmailmsg"><<a href="mailto:mayabritstein@gmail.com" target="_blank">mayabritstein@gmail.com</a>></span> 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"><span style="font-size:10.5pt;font-family:Calibri;color:black">Hi,
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">I have RNA-seq data, and genomic data that I want to annotate using maker. <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">From what I understood, I need to genarate a gff3 file format from the RNA-seq mapping sequences. I had mapped the RNA sequences to the genome using bowtie and tophat. However,
I still do not know how to take these format and convert them to a gff3 file that I can them use in maker as annotation evidence <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">I saw the wiki page, that did not mention how to make this conversion (<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_wiki_GFF3&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=OMPcIr8gCZc0MtV0NaCwpEmyn1zMeLOzW7v7LAyAcDU&s=B1gZmgsg06xIvtRwdOwnNvYzLU-obgTch1fU0jWhy9w&e=" target="_blank">http://gmod.org/wiki/GFF3</a>)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">Can you please help me?<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">Sincerely,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">Maya<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal" align="right" dir="RTL" style="text-align:left;direction:rtl;unicode-bidi:embed">
<span dir="RTL"></span><span lang="AR-SA" style="font-size:10.5pt;color:black"><span dir="RTL"></span>----</span><span dir="LTR" style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
<div>
<p class="MsoNormal" align="right" dir="RTL" style="text-align:left;direction:rtl;unicode-bidi:embed">
<span dir="LTR" style="font-size:9.5pt;font-family:Calibri;color:black">Maya Britstein</span><span lang="AR-SA" style="font-size:9.5pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" align="right" dir="RTL" style="text-align:left;direction:rtl;unicode-bidi:embed">
<span dir="LTR" style="font-size:9.5pt;font-family:Calibri;color:black">Ph.D candidate</span><span lang="AR-SA" style="font-size:9.5pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" align="right" dir="RTL" style="text-align:left;direction:rtl;unicode-bidi:embed">
<span dir="LTR" style="font-size:9.5pt;font-family:Calibri;color:black">Laura Steindler's Lab</span><span lang="AR-SA" style="font-size:9.5pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" align="right" dir="RTL" style="text-align:left;direction:rtl;unicode-bidi:embed">
<span dir="LTR" style="font-size:9.5pt;font-family:Calibri;color:black">Marine Biology Department</span><span lang="AR-SA" style="font-size:9.5pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" align="right" dir="RTL" style="text-align:left;direction:rtl;unicode-bidi:embed">
<span dir="LTR" style="font-size:9.5pt;font-family:Calibri;color:black">Leon H. Charney School of Marine Sciences</span><span lang="AR-SA" style="font-size:9.5pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" align="right" dir="RTL" style="text-align:left;direction:rtl;unicode-bidi:embed">
<span dir="LTR" style="font-size:9.5pt;font-family:Calibri;color:black">University of Haifa, Israel</span><span lang="AR-SA" style="font-size:9.5pt;color:black"><o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><span lang="AR-SA" dir="RTL" style="font-size:10.5pt;color:black"><o:p> </o:p></span></p>
</div>
</div>
</blockquote>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><br>
<br clear="all">
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">--
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">------------------------------------------------------------------------<br>
Scott Cain, Ph. D. scott at scottcain dot net<br>
GMOD Coordinator (<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=OMPcIr8gCZc0MtV0NaCwpEmyn1zMeLOzW7v7LAyAcDU&s=wb5XMrtNYBOrAngXKEi9GdfppioFQ3nnLiJvcdP1jLo&e=" target="_blank">http://gmod.org/</a>)
216-392-3087<br>
Ontario Institute for Cancer Research<o:p></o:p></span></p>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<p class="MsoNormal">_______________________________________________<br>
maker-devel mailing list<br>
<a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a><br>
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=nDcMZi8LwiKXV-94ieW6tG0bEcaZof1aYjvJpMNjDME&s=kb8B_j9O5us3LoI3siiGDenax1ptk_GUX1LqjlB0S4U&e=" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><o:p></o:p></p>
</blockquote>
</div>
<div>
<p class="MsoNormal">-- <o:p></o:p></p>
</div>
<div>
<p>____________________________<br>
Sent from Inbox Mobile<o:p></o:p></p>
</div>
</div>
</body>
</html>