<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="">Hi Jia-Xing,<div class=""><br class=""></div><div class="">That has been my experience in the past as well. For the non-coding RNAs tRNA-scan is very accurate while snoscan seems to be quite sensitive but very specific. Did you give it a “snoscan_meth” file? Giving it a snoscan_meth file will help with accuracy. The biggest gains in accuracy are from small RNA-seq data. In the paper where we used snoscan on maize we didn’t keep any snoRNA predictions that didn’t have support from small RNA-seq data, in practical terms we got rid of anything with a AED of 1.</div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Mike<br class=""><div><blockquote type="cite" class=""><div class="">On May 15, 2017, at 7:28 AM, Jia-Xing Yue <<a href="mailto:yuejiaxing@gmail.com" class="">yuejiaxing@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class="">Hello,<br class=""><br class=""></div>I configured snoscan (v.0.9.1) for my maker installation (v2.31.9) and run the annotation for a yeast (S. cerevisiae) genome. I think the annotation went well with regard to tRNAs and protein-coding genes but I am not sure about snoRNAs. I found multiple overlapped snoRNA genes were annotated by maker as the example below shows. I was wondering if this is expected. If not, what might have caused this problem and is there a way to work around. Thanks in advance!<br class=""><br class="">chrIX maker gene 4328 4416 . + . ID=snoscan-chrIX-noncoding-gene-0.49;Name=snoscan-chrIX-noncoding-gene-0.49<br class="">chrIX maker snoRNA 4328 4416 . + . ID=snoscan-chrIX-noncoding-gene-0.49-snoRNA-1;Parent=snoscan-chrIX-noncoding-gene-0.49;Name=snoscan-chrIX-noncoding-gene-0.49-snoRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|0|1|90|0<br class="">chrIX maker exon 4328 4416 . + . ID=snoscan-chrIX-noncoding-gene-0.49-snoRNA-1:exon:12260;Parent=snoscan-chrIX-noncoding-gene-0.49-snoRNA-1<br class="">chrIX maker gene 4375 4563 . + . ID=snoscan-chrIX-noncoding-gene-0.50;Name=snoscan-chrIX-noncoding-gene-0.50<br class="">chrIX maker snoRNA 4375 4563 . + . ID=snoscan-chrIX-noncoding-gene-0.50-snoRNA-1;Parent=snoscan-chrIX-noncoding-gene-0.50;Name=snoscan-chrIX-noncoding-gene-0.50-snoRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|0|1|190|0<br class="">chrIX maker exon 4375 4563 . + . ID=snoscan-chrIX-noncoding-gene-0.50-snoRNA-1:exon:12261;Parent=snoscan-chrIX-noncoding-gene-0.50-snoRNA-1<br class="">chrIX maker gene 4375 4461 . + . ID=snoscan-chrIX-noncoding-gene-0.51;Name=snoscan-chrIX-noncoding-gene-0.51<br class="">chrIX maker snoRNA 4375 4461 . + . ID=snoscan-chrIX-noncoding-gene-0.51-snoRNA-1;Parent=snoscan-chrIX-noncoding-gene-0.51;Name=snoscan-chrIX-noncoding-gene-0.51-snoRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|0|1|88|0<br class="">chrIX maker exon 4375 4461 . + . ID=snoscan-chrIX-noncoding-gene-0.51-snoRNA-1:exon:12262;Parent=snoscan-chrIX-noncoding-gene-0.51-snoRNA-1<br class="">chrIX maker gene 4375 4491 . + . ID=snoscan-chrIX-noncoding-gene-0.52;Name=snoscan-chrIX-noncoding-gene-0.52<br class="">chrIX maker snoRNA 4375 4491 . + . ID=snoscan-chrIX-noncoding-gene-0.52-snoRNA-1;Parent=snoscan-chrIX-noncoding-gene-0.52;Name=snoscan-chrIX-noncoding-gene-0.52-snoRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|0|1|118|0<br class="">chrIX maker exon 4375 4491 . + . ID=snoscan-chrIX-noncoding-gene-0.52-snoRNA-1:exon:12263;Parent=snoscan-chrIX-noncoding-gene-0.52-snoRNA-1<br class="">chrIX maker gene 4375 4500 . + . ID=snoscan-chrIX-noncoding-gene-0.53;Name=snoscan-chrIX-noncoding-gene-0.53<br class="">chrIX maker snoRNA 4375 4500 . + . ID=snoscan-chrIX-noncoding-gene-0.53-snoRNA-1;Parent=snoscan-chrIX-noncoding-gene-0.53;Name=snoscan-chrIX-noncoding-gene-0.53-snoRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|0|1|127|0<br class="">chrIX maker exon 4375 4500 . + . ID=snoscan-chrIX-noncoding-gene-0.53-snoRNA-1:exon:12264;Parent=snoscan-chrIX-noncoding-gene-0.53-snoRNA-1<br class=""><br class=""></div>Best,<br class=""></div>Jia-Xing<br class=""><div class=""><div class=""><br clear="all" class=""><div class=""><div class=""><br class="">-- <br class=""><div class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><span style="" class="">Jia-Xing Yue <br class=""><br class=""></span></div><div class=""><span style="" class="">Population Genomics and Complex Traits Group</span></div><div class=""><span style="" class=""><font face="arial, helvetica, sans-serif" size="2" class="">Tour Pasteur 8eme etage</font></span><span style="" class=""><div class=""><font face="arial, helvetica, sans-serif" size="2" class="">Faculté de Médecine<br class=""></font><span class=""><div class=""><font face="arial, helvetica, sans-serif" size="2" class="">Institute for Research on Cancer and Aging, Nice (IRCAN)</font></div><div class=""><font face="arial, helvetica, sans-serif" size="2" class="">CNRS UMR 7284 - INSERM U 1081 - </font>Université Côte d’Azur (UCA)</div></span><font face="arial, helvetica, sans-serif" size="2" class="">28 Avenue de Valombrose</font></div><div class=""><font face="arial, helvetica, sans-serif" size="2" class="">06107 NICE Cedex 2</font></div><div class=""><font face="arial, helvetica, sans-serif" size="2" class="">France</font></div></span><br class=""></div><div class=""><div class="">Personal website: <a href="http://www.iamphioxus.org/" target="_blank" class="">http://www.iamphioxus.org/</a><br class=""><br class=""></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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