<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="">(1) De novo assembly without mapping to any genome assembly (like Trinity)<div class=""><br class=""></div><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><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 9:13 AM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com" class="">qwzhang0601@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class="">Hello: <br class=""><br class="">
<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. <br class="">(1) De novo assembly without mapping to any genome assembly (like Trinity)?<br class=""></span></div><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=""><br class=""></span></div><span style="font-size:12pt;font-family:cambria" class="">Thanks<br class=""><br class=""></span></div><span style="font-size:12pt;font-family:cambria" class="">Best<br class=""></span></div><span style="font-size:12pt;font-family:cambria" class="">Quanwei<br class=""></span><div class=""><div class=""><div class=""><div class=""> <br class=""></div></div></div></div></div>
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