<div dir="ltr"><div><div><div><div>Hi Michael,<br><br></div>Many thanks for the information! I will specify the "snoscan_meth" file and give it another try then. I majorly want to use maker to annotate protein-coding genes and tRNAs. But it would be nice to have snoRNA reasonably annotated as well. <br></div>Thanks gain and have a great day!<br><br></div>Best,<br></div>Jia-Xing<br><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, May 15, 2017 at 6:28 PM, Michael Campbell <span dir="ltr"><<a href="mailto:michael.s.campbell1@gmail.com" target="_blank">michael.s.campbell1@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Jia-Xing,<div><br></div><div>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><br></div><div>I hope this helps,</div><div>Mike<br><div><blockquote type="cite"><div><div class="h5"><div>On May 15, 2017, at 7:28 AM, Jia-Xing Yue <<a href="mailto:yuejiaxing@gmail.com" target="_blank">yuejiaxing@gmail.com</a>> wrote:</div><br class="m_-7608062531693256888Apple-interchange-newline"></div></div><div><div><div class="h5"><div dir="ltr"><div><div><div>Hello,<br><br></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><br>chrIX maker gene 4328 4416 . + . ID=snoscan-chrIX-noncoding-<wbr>gene-0.49;Name=snoscan-chrIX-<wbr>noncoding-gene-0.49<br>chrIX maker snoRNA 4328 4416 . + . ID=snoscan-chrIX-noncoding-<wbr>gene-0.49-snoRNA-1;Parent=<wbr>snoscan-chrIX-noncoding-gene-<wbr>0.49;Name=snoscan-chrIX-<wbr>noncoding-gene-0.49-snoRNA-1;_<wbr>AED=1.00;_eAED=1.00;_QI=0|-1|<wbr>0|0|-1|0|1|90|0<br>chrIX maker exon 4328 4416 . + . ID=snoscan-chrIX-noncoding-<wbr>gene-0.49-snoRNA-1:exon:12260;<wbr>Parent=snoscan-chrIX-<wbr>noncoding-gene-0.49-snoRNA-1<br>chrIX maker gene 4375 4563 . + . ID=snoscan-chrIX-noncoding-<wbr>gene-0.50;Name=snoscan-chrIX-<wbr>noncoding-gene-0.50<br>chrIX maker snoRNA 4375 4563 . + . ID=snoscan-chrIX-noncoding-<wbr>gene-0.50-snoRNA-1;Parent=<wbr>snoscan-chrIX-noncoding-gene-<wbr>0.50;Name=snoscan-chrIX-<wbr>noncoding-gene-0.50-snoRNA-1;_<wbr>AED=1.00;_eAED=1.00;_QI=0|-1|<wbr>0|0|-1|0|1|190|0<br>chrIX maker exon 4375 4563 . + . ID=snoscan-chrIX-noncoding-<wbr>gene-0.50-snoRNA-1:exon:12261;<wbr>Parent=snoscan-chrIX-<wbr>noncoding-gene-0.50-snoRNA-1<br>chrIX maker gene 4375 4461 . + . ID=snoscan-chrIX-noncoding-<wbr>gene-0.51;Name=snoscan-chrIX-<wbr>noncoding-gene-0.51<br>chrIX maker snoRNA 4375 4461 . + . ID=snoscan-chrIX-noncoding-<wbr>gene-0.51-snoRNA-1;Parent=<wbr>snoscan-chrIX-noncoding-gene-<wbr>0.51;Name=snoscan-chrIX-<wbr>noncoding-gene-0.51-snoRNA-1;_<wbr>AED=1.00;_eAED=1.00;_QI=0|-1|<wbr>0|0|-1|0|1|88|0<br>chrIX maker exon 4375 4461 . + . ID=snoscan-chrIX-noncoding-<wbr>gene-0.51-snoRNA-1:exon:12262;<wbr>Parent=snoscan-chrIX-<wbr>noncoding-gene-0.51-snoRNA-1<br>chrIX maker gene 4375 4491 . + . ID=snoscan-chrIX-noncoding-<wbr>gene-0.52;Name=snoscan-chrIX-<wbr>noncoding-gene-0.52<br>chrIX maker snoRNA 4375 4491 . + . ID=snoscan-chrIX-noncoding-<wbr>gene-0.52-snoRNA-1;Parent=<wbr>snoscan-chrIX-noncoding-gene-<wbr>0.52;Name=snoscan-chrIX-<wbr>noncoding-gene-0.52-snoRNA-1;_<wbr>AED=1.00;_eAED=1.00;_QI=0|-1|<wbr>0|0|-1|0|1|118|0<br>chrIX maker exon 4375 4491 . + . ID=snoscan-chrIX-noncoding-<wbr>gene-0.52-snoRNA-1:exon:12263;<wbr>Parent=snoscan-chrIX-<wbr>noncoding-gene-0.52-snoRNA-1<br>chrIX maker gene 4375 4500 . + . ID=snoscan-chrIX-noncoding-<wbr>gene-0.53;Name=snoscan-chrIX-<wbr>noncoding-gene-0.53<br>chrIX maker snoRNA 4375 4500 . + . ID=snoscan-chrIX-noncoding-<wbr>gene-0.53-snoRNA-1;Parent=<wbr>snoscan-chrIX-noncoding-gene-<wbr>0.53;Name=snoscan-chrIX-<wbr>noncoding-gene-0.53-snoRNA-1;_<wbr>AED=1.00;_eAED=1.00;_QI=0|-1|<wbr>0|0|-1|0|1|127|0<br>chrIX maker exon 4375 4500 . + . ID=snoscan-chrIX-noncoding-<wbr>gene-0.53-snoRNA-1:exon:12264;<wbr>Parent=snoscan-chrIX-<wbr>noncoding-gene-0.53-snoRNA-1<br><br></div>Best,<br></div>Jia-Xing<br><div><div><br clear="all"><div><div><br>-- <br><div class="m_-7608062531693256888gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><span>Jia-Xing Yue <br><br></span></div><div><span>Population Genomics and Complex Traits Group</span></div><div><span><font face="arial, helvetica, sans-serif" size="2">Tour Pasteur 8eme etage</font></span><span><div><font face="arial, helvetica, sans-serif" size="2">Faculté de Médecine<br></font><span><div><font face="arial, helvetica, sans-serif" size="2">Institute for Research on Cancer and Aging, Nice (IRCAN)</font></div><div><font face="arial, helvetica, sans-serif" size="2">CNRS UMR 7284 - INSERM U 1081 - </font>Université Côte d’Azur (UCA)</div></span><font face="arial, helvetica, sans-serif" size="2">28 Avenue de Valombrose</font></div><div><font face="arial, helvetica, sans-serif" size="2">06107 NICE Cedex 2</font></div><div><font face="arial, helvetica, sans-serif" size="2">France</font></div></span><br></div><div><div>Personal website: <a href="http://www.iamphioxus.org/" target="_blank">http://www.iamphioxus.org/</a><br><br></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
</div></div></div></div></div></div></div>
______________________________<wbr>_________________<br>maker-devel mailing list<br><a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.<wbr>com</a><br><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/<wbr>mailman/listinfo/maker-devel_<wbr>yandell-lab.org</a><br></div></blockquote></div><br></div></div></blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><span style="color:rgb(0,0,0)">Jia-Xing Yue <br><br></span></div><div><span style="color:rgb(0,0,0)">Population Genomics and Complex Traits Group</span></div><div><span style="color:rgb(0,0,0)"><font size="2" face="arial, helvetica, sans-serif">Tour Pasteur 8eme etage</font></span><span style="color:rgb(0,0,0)"><div><font size="2" face="arial, helvetica, sans-serif">Faculté de Médecine<br></font><span><div><font size="2" face="arial, helvetica, sans-serif">Institute for Research on Cancer and Aging, Nice (IRCAN)</font></div><div><font size="2" face="arial, helvetica, sans-serif">CNRS UMR 7284 - INSERM U 1081 - </font>Université Côte d’Azur (UCA)</div></span><font size="2" face="arial, helvetica, sans-serif">28 Avenue de Valombrose</font></div><div><font size="2" face="arial, helvetica, sans-serif">06107 NICE Cedex 2</font></div><div><font size="2" face="arial, helvetica, sans-serif">France</font></div></span><br></div><div><div>Personal website: <a href="http://www.iamphioxus.org/" target="_blank">http://www.iamphioxus.org/</a><br><br></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
</div>