<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>There will be no negative effects in restarting. The min_contig option just speeds things up by skipping contigs that are likely too small to accurately annotate. Gene predictors generally require a certain amount of sequence upstream and downstream of a gene to work accurately, so for most Eukaryotic organisms, contigs of size of less than 10,000 will not produce results, but if the genes are smaller in your organism you can reduce this. The basic idea is to just skip contigs that won't produce results anyways.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></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> Diego Calderon <<a href="mailto:dcalderon@wesleyan.edu">dcalderon@wesleyan.edu</a>><br><span style="font-weight:bold">Date: </span> Monday, 9 July, 2012 7:20 PM<br><span style="font-weight:bold">To: </span> 李青 Li, Qing <<a href="mailto:liqing850104@gmail.com">liqing850104@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> Re: Help: min_contig length<br></div><div><br></div>Just a little add on:<br>If we stop the currently running mpi maker, change the option from the default 1 to 500 or 1000, then restart maker, will it have any (negative) effect on maker (for example having to restart the analysis or something)?<br><br>I'm guessing that it will not, but we just wanted to make sure.<br><br>Best,<br>Diego<br><br><br><div class="gmail_quote">On Mon, Jul 9, 2012 at 5:11 PM, 李青 Li, Qing <span dir="ltr"><<a href="mailto:liqing850104@gmail.com" target="_blank">liqing850104@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Carson,<div>Very sorry for disturbing you! Diego and I are running maker for whole genome annotation now, and we have a question: should the min_contig=500 or 1000? We asked several people but get different answers,,, So we think you may be the best one to ask,,,</div><div>Thank you!</div><div>Best,</div><div>Qing</div></blockquote></div><br></span></body></html>