<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">No. My experience has just been with regular Trinity de novo assembly. Of course, I’d be interested in any one else’s attempt at this though.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jan 27, 2017, at 3:21 PM, Fields, Christopher J <<a href="mailto:cjfields@illinois.edu" class="">cjfields@illinois.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div class="">Yup I agree. Carson, would you know of any instances where HiSAT2/STAR+Stringtie or reference-based Trinity assemblies were (successfully) used? </div>
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<div class="">chris</div>
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<span style="font-weight:bold" class="">From: </span>maker-devel <<a href="mailto:maker-devel-bounces@yandell-lab.org" class="">maker-devel-bounces@yandell-lab.org</a>> on behalf of Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>><br class="">
<span style="font-weight:bold" class="">Date: </span>Friday, January 27, 2017 at 10:23 AM<br class="">
<span style="font-weight:bold" class="">To: </span>Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com" class="">qwzhang0601@gmail.com</a>><br class="">
<span style="font-weight:bold" class="">Cc: </span>"<a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a>><br class="">
<span style="font-weight:bold" class="">Subject: </span>Re: [maker-devel] transcript assembly of RNA-seq data<br class="">
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(1) De novo assembly without mapping to any genome assembly (like Trinity)
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<div class="">You get a lower false positive rate (TopHat+Cufflink is too noisy). And protein evidence will make up for any loss of sensitivity associated with the De novo assembly path. Make sure to us the jaccard_clip option to reduce transcript merging
in Trinity.</div>
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<div class="">On Jan 27, 2017, at 9:13 AM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com" class="">qwzhang0601@gmail.com</a>> wrote:</div>
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<div class="">Hello: <br class="">
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<span style="font-size:12pt;font-family:cambria" class="">I wonder which is the best way to make use of RNA-seq data for gene annotation of a new genome assembly.
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(1) De novo assembly without mapping to any genome assembly (like Trinity)?<br class="">
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<span style="font-size:12pt;font-family:cambria" class="">(2) TopHat+Cufflink do mapping to the new
</span><span style="font-size:12pt;font-family:cambria" class="">genome assembly, that want to annotate?<br class="">
(3) </span><span style="font-size:12pt;font-family:cambria" class="">TopHat+Cufflink do mapping to a close annotated genome (like mouse or human)?<br class="">
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<span style="font-size:12pt;font-family:cambria" class="">Thanks<br class="">
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<span style="font-size:12pt;font-family:cambria" class="">Best<br class="">
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<span style="font-size:12pt;font-family:cambria" class="">Quanwei<br class="">
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