<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>1. I'm wondering if MAKER will take into account both types of evidence? </div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Yes.</div><div><br></div><div>2. Would it be better to merge both PASA and cufflinks gff3s using gff3_merge? </div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>You can provide them as a comma separated list of files to the est_gff= option, or you can merge them using the gff3_merge script that comes with MAKER.</div><div><br></div><div>Unfortunately I have no one best option for which evidence types to include. Every evidence type can contribute in it's own way to the final results. When you test using different evidence types, try running on a single large contig and manually view the results in a browser.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; 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"><span style="font-weight:bold">From: </span> Selene Lizbeth Fernandez Valverde <<a href="mailto:uqslizbe@uq.edu.au">uqslizbe@uq.edu.au</a>><br><span style="font-weight:bold">Date: </span> Thursday, September 5, 2013 3:30 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Maker: Question on using both Trinity and Cufflinks<br></div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><font class="Apple-style-span">Hi all, </font></div><div><br></div><div>I'm currently using Maker to reannotate the genome of the marine sponge. We already have a set of Augustus prediction and gene models that I mapped back to the genome using the patched map2assembly script posted on the mailing list, as well as PASA transcripts (based on Trinity assemblies) and cufflinks transcripts. </div><div><br></div><div>I would like to include<b> both</b> Trinity and Cufflinks, as in some cases one outperforms the other. </div><div><br></div><div>I'm currently planning to provide the Trinity/PASA assemblies as fasta to the "est" option and the cufflinks assemblies as gff3 using the "est_gff" option but I'm wondering if MAKER will take into account both types of evidence? Would it be better to merge both PASA and cufflinks gff3s using gff3_merge? </div><div><br></div><div style="font-family: Times; "><span class="Apple-style-span" style="font-size: 12px; font-family: Helvetica; ">Thanks in advance for the advice, </span></div><div><br></div><div>Selene</div><div><br></div><div><br></div><div><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none; ">**est_gff/est --> These are assumed to be correctly assembled and aligned</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);"><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none; ">around splice sites (MAKER uses exonerate to align around splice sites for</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);"><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none; ">ESTs in FASTA files). MAKER can use them to infer gene models directly</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);"><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none; ">(est2genome option), can use them as support for maintaining predictions,</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);"><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none; ">and can use them to modify structure and add UTR to predictions. If you</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);"><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none; ">let MAKER try and find alternative splice forms, they will be used to</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);"><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none; ">identify support for splice variants. How these cluster with other</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);"><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none; ">evidence will help MAKER infer gene boundaries in some cases. MAKER will</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);"><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none; ">also use splice sites inferred from the ESTs to inform gene predictors</span><br style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);"><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none; ">during the prediction step.</span></div><div><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none; "><br></span></div><div><span style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none; "><br></span></div><div style="font-family: Times; "><span class="Apple-style-span" style="font-size: 12px; font-family: Helvetica; "><br></span></div><div style="font-family: Times; "><span class="Apple-style-span" style="font-size: 12px; font-family: Helvetica; ">Selene Fernandez-Valverde Ph.D.</span></div><div apple-content-edited="true"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div style="font-size: 12px; ">Postdoctoral Research Fellow</div></div></div></span></div></div><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div style="font-size: 12px; ">School of Biological Sciences</div><div style="font-size: 12px; ">University of Queensland</div><div style="font-size: 12px; ">St Lucia QLD 4072</div><div style="font-size: 12px; ">Australia</div><div style="font-size: 12px; "><a href="mailto:uqslizbe@uq.edu.au">uqslizbe@uq.edu.au</a></div></div></div></span></div></span></div></span></div><br></div></div>_______________________________________________
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