<p dir="ltr">Hi Christopher,</p>
<p dir="ltr">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? </p>
<p dir="ltr">Best<br>
/SB</p>
<br><div class="gmail_quote"><div dir="ltr">On Thu, 26 Jan 2017, 01:04 Fields, Christopher J, <<a href="mailto:cjfields@illinois.edu">cjfields@illinois.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif" class="gmail_msg">
<div class="gmail_msg">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. </div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg">chris </div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
<span id="m_-1351972388141770776OLK_SRC_BODY_SECTION" class="gmail_msg">
<div style="font-family:Calibri;font-size:12pt;text-align:left;color:black;BORDER-BOTTOM:medium none;BORDER-LEFT:medium none;PADDING-BOTTOM:0in;PADDING-LEFT:0in;PADDING-RIGHT:0in;BORDER-TOP:#b5c4df 1pt solid;BORDER-RIGHT:medium none;PADDING-TOP:3pt" class="gmail_msg">
<span style="font-weight:bold" class="gmail_msg">From: </span>maker-devel <<a href="mailto:maker-devel-bounces@yandell-lab.org" class="gmail_msg" target="_blank">maker-devel-bounces@yandell-lab.org</a>> on behalf of Scott Cain <<a href="mailto:scott@scottcain.net" class="gmail_msg" target="_blank">scott@scottcain.net</a>><br class="gmail_msg">
<span style="font-weight:bold" class="gmail_msg">Date: </span>Wednesday, January 25, 2017 at 2:23 PM<br class="gmail_msg">
<span style="font-weight:bold" class="gmail_msg">To: </span>Maya Britstein <<a href="mailto:mayabritstein@gmail.com" class="gmail_msg" target="_blank">mayabritstein@gmail.com</a>><br class="gmail_msg">
<span style="font-weight:bold" class="gmail_msg">Cc: </span>"<a href="mailto:maker-devel@yandell-lab.org" class="gmail_msg" target="_blank">maker-devel@yandell-lab.org</a> List" <<a href="mailto:maker-devel@yandell-lab.org" class="gmail_msg" target="_blank">maker-devel@yandell-lab.org</a>>, "<a href="mailto:help@gmod.org" class="gmail_msg" target="_blank">help@gmod.org</a>"
<<a href="mailto:help@gmod.org" class="gmail_msg" target="_blank">help@gmod.org</a>><br class="gmail_msg">
<span style="font-weight:bold" class="gmail_msg">Subject: </span>Re: [maker-devel] GFF3 file format<br class="gmail_msg">
</div></span></div><div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif" class="gmail_msg"><span id="m_-1351972388141770776OLK_SRC_BODY_SECTION" class="gmail_msg">
<div class="gmail_msg"><br class="gmail_msg">
</div>
<blockquote id="m_-1351972388141770776MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT:#b5c4df 5 solid;PADDING:0 0 0 5;MARGIN:0 0 0 5" class="gmail_msg">
<div class="gmail_msg">
<div class="gmail_msg">
<div dir="ltr" class="gmail_msg">Hi Maya,
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg">I'm not sure what MAKER's requirements are in this regard--I'm forwarding this to their mailing list.</div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg">Scott</div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
</div>
<div class="gmail_extra gmail_msg"><br class="gmail_msg">
<div class="gmail_quote gmail_msg">On Wed, Jan 25, 2017 at 3:12 PM, Maya Britstein <span dir="ltr" class="gmail_msg">
<<a href="mailto:mayabritstein@gmail.com" class="gmail_msg" target="_blank">mayabritstein@gmail.com</a>></span> wrote:<br class="gmail_msg">
<blockquote class="gmail_quote gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" class="gmail_msg">Hi,
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg">I have RNA-seq data, and genomic data that I want to annotate using maker. </div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg">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 </div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg">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=" class="gmail_msg" target="_blank">http://gmod.org/wiki/GFF3</a>)</div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg">Can you please help me?</div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg">Sincerely,</div>
<div class="gmail_msg">Maya</div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg">
<div dir="ltr" class="gmail_msg">
<div dir="rtl" style="text-align:left" class="gmail_msg">----<br class="gmail_msg">
</div>
<div dir="rtl" class="gmail_msg">
<div style="text-align:left;font-size:12.8px" class="gmail_msg">Maya Britstein</div>
<div style="text-align:left;font-size:12.8px" class="gmail_msg">Ph.D candidate</div>
<div style="text-align:left;font-size:12.8px" class="gmail_msg">Laura Steindler's Lab</div>
<div style="text-align:left;font-size:12.8px" class="gmail_msg">Marine Biology Department</div>
<div style="text-align:left;font-size:12.8px" class="gmail_msg">Leon H. Charney School of Marine Sciences</div>
<div style="text-align:left;font-size:12.8px" class="gmail_msg">University of Haifa, Israel</div>
</div>
</div>
<br class="gmail_msg">
</div>
</div>
</blockquote>
</div>
<br class="gmail_msg">
<br clear="all" class="gmail_msg">
<div class="gmail_msg"><br class="gmail_msg">
</div>
-- <br class="gmail_msg">
<div class="m_-1351972388141770776gmail_signature gmail_msg" data-smartmail="gmail_signature">------------------------------------------------------------------------<br class="gmail_msg">
Scott Cain, Ph. D. scott at scottcain dot net<br class="gmail_msg">
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=" class="gmail_msg" target="_blank">http://gmod.org/</a>)
216-392-3087<br class="gmail_msg">
Ontario Institute for Cancer Research</div>
</div>
</div>
</div>
</blockquote>
</span></div>
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