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<div>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>
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<div>chris </div>
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<span style="font-weight:bold">From: </span>maker-devel <<a href="mailto:maker-devel-bounces@yandell-lab.org">maker-devel-bounces@yandell-lab.org</a>> on behalf of Scott Cain <<a href="mailto:scott@scottcain.net">scott@scottcain.net</a>><br>
<span style="font-weight:bold">Date: </span>Wednesday, January 25, 2017 at 2:23 PM<br>
<span style="font-weight:bold">To: </span>Maya Britstein <<a href="mailto:mayabritstein@gmail.com">mayabritstein@gmail.com</a>><br>
<span style="font-weight:bold">Cc: </span>"<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a> List" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>>, "<a href="mailto:help@gmod.org">help@gmod.org</a>"
<<a href="mailto:help@gmod.org">help@gmod.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] GFF3 file format<br>
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<div dir="ltr">Hi Maya,
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<div>I'm not sure what MAKER's requirements are in this regard--I'm forwarding this to their mailing list.</div>
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<div>Scott</div>
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<div class="gmail_quote">On Wed, Jan 25, 2017 at 3:12 PM, Maya Britstein <span dir="ltr">
<<a href="mailto:mayabritstein@gmail.com" target="_blank">mayabritstein@gmail.com</a>></span> wrote:<br>
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<div dir="ltr">Hi,
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<div>I have RNA-seq data, and genomic data that I want to annotate using maker. </div>
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<div>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>
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<div>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>)</div>
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<div>Can you please help me?</div>
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<div>Sincerely,</div>
<div>Maya</div>
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<div dir="rtl" style="text-align:left">----<br>
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<div style="text-align:left;font-size:12.8px">Maya Britstein</div>
<div style="text-align:left;font-size:12.8px">Ph.D candidate</div>
<div style="text-align:left;font-size:12.8px">Laura Steindler's Lab</div>
<div style="text-align:left;font-size:12.8px">Marine Biology Department</div>
<div style="text-align:left;font-size:12.8px">Leon H. Charney School of Marine Sciences</div>
<div style="text-align:left;font-size:12.8px">University of Haifa, Israel</div>
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-- <br>
<div class="gmail_signature" data-smartmail="gmail_signature">------------------------------------------------------------------------<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</div>
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