<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="">MAKER will report back all positions. The value in the score column can be used to see how well they match the original (range between 0 and 100). In the event of a tie, you will need to manually select one or the other. The process of mapping onto a new assembly is unfortunately not completely automated. It still requires intervention from the user in those cases.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Apr 4, 2016, at 10:40 AM, 陈文博 <<a href="mailto:chenwenbo1020@gmail.com" class="">chenwenbo1020@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Carson,<div class=""><br class=""></div><div class="">Thank you. </div><div class=""><br class=""></div><div class="">sorry that I forgot to mention that in the new version assembly I only connected some scaffolds into super scaffold by Ns. </div><div class=""><br class=""></div><div class="">Annotation question is :</div><div class=""><br class=""></div><div class="">Maker use blast to anchor the gene. If some genes were mapped to multiple positions (for example single-exon genes), what will Maker decide to do?</div><div class=""><br class=""></div><div class="">Thanks!</div><div class=""><br class=""></div><div class="">Best,</div><div class="">Wenbo</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">2016-04-04 12:34 GMT-04:00 Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Because the assembly has changed. That means that sequence can be different, missing, or altered to break previous CDS. You can try relaxing the filtering parameters in maker_bopts.ctl to recover more partial or incomplete matches. Also adjust the mx intron size to allow for really long introns. That might recover a few more.<br class="">
<br class="">
—Carson<br class="">
<div class=""><div class="h5"><br class="">
<br class="">
<br class="">
> On Apr 2, 2016, at 5:41 PM, 陈文博 <<a href="mailto:chenwenbo1020@gmail.com" class="">chenwenbo1020@gmail.com</a>> wrote:<br class="">
><br class="">
> Hi All,<br class="">
><br class="">
> Recently, I updated the genome assembly, and want to update the annotation to fit the new genome, only want to update the gene position. I used Maker. I changed the maker_opt.ctl file as follow:<br class="">
><br class="">
> genome=$PATH_TO_mygenome<br class="">
><br class="">
> organism_type=eukaryotic<br class="">
><br class="">
> est=$PATH_TO_transcript_seq<br class="">
><br class="">
> est2genome=1<br class="">
><br class="">
><br class="">
> est_forward=1<br class="">
><br class="">
> After run Maker, some genes were lost. There are 14,146 transcritpts as input. Only 13092 gene models were in the output. Anyone know the reason? Thank you!<br class="">
><br class="">
> Best regards,<br class="">
> Wenbo<br class="">
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