<div dir="ltr"><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">Dear Carson</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent"><br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr"></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">I am subscribed to the Maker list, but for some reason I cannot post a new topic when I view the Forum page. I hope it is OK if I email you directly?</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent"><br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr"></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">I am trying to annotate a newly sequenced genome.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">I have RNAseq data, a species specific repeat library that was generated with REPET, the unmasked genome, and proteins from a "closley" related species (actually not that close, but my species is the only one in its genus, so I took proteins from another genus in the same family).</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent"><br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr"></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">I started by following Support Protocol 1, on page 10 of the article "Genome annotation and Curation using MAKER and MAKER-P" published in Curr Protoc Bioinformatics 48.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent"><br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr"></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">The input that I used for generating the gene models (before training SNAP) was:</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">the est data, my genome and the protein data. I also set est2genome=1 and protein2genome=1. I also used Repeat masking and included my species specific repeat library.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">softmasking was set to 1</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">That output was used to train snap. <br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr"></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent"><br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr"></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">Then I ran maker in "Gene prediction mode" as outlined on page 11 using the hmm file as input (and setting est2genome=0 and protein2genome=0). Repeat masking was enabled, again using my species specific library.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent"><br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr"></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">I trained snap for a second time.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">That output was used as input for Basic Protocol 1 on page 3 of the aforementioned article.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">Input for Basic Protocol 1 was:</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">The snap hmm file</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">my unmasked genome</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">the species specific repeat library</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">RNAseq evidence</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">the protein evidence from a close relative</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">softmasking was set to 1</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">est2genome=0</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">protein2genome=0</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent"><br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr"></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">I collected the results as outlined on page 5 of the article.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">However I noticed that there were no Fasta files.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">Do you have any idea what could have gone wrong?</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">Can I send my log files to you? Thanks in advance for any assistance.</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent"><br style="margin:0px;padding-bottom:0px;font-size:12.8px;direction:ltr"></div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">Kind Regards</div><div style="margin:0px;text-align:left;color:rgb(34,34,34);text-transform:none;text-indent:0px;letter-spacing:normal;padding-bottom:0px;font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:400;text-decoration:none;word-spacing:0px;white-space:normal;direction:ltr;background-color:transparent">Anna Yssel</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 12 April 2018 at 10:16, Ansie Yssel <span dir="ltr"><<a href="mailto:aejysselansie@gmail.com" target="_blank">aejysselansie@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 dir="ltr"><div>Dear Carson</div><div><br></div><div>I am subscribed to the Maker list, but for some reason I cannot post a new topic when I view the Forum page. I hope it is OK if I email you directly?</div><div><br></div><div>I am trying to annotate a newly sequenced genome.</div><div>I have RNAseq data, a species specific repeat library that was generated with REPET, the unmasked genome, and proteins from a "closley" related species (actually not that close, but my species is the only one in its genus, so I took proteins from another genus in the same family).</div><div><br></div><div>I started by following Support Protocol 1, on page 10 of the article "Genome annotation and Curation using MAKER and MAKER-P" published in Curr Protoc Bioinformatics 48.</div><div><br></div><div>The input that I used for generating the gene models (before training SNAP) was:</div><div>the est data, my genome and the protein data. I also set est2genome=1 and protein2genome=1. I also used Repeat masking and included my species specific repeat library.</div><div>softmasking was set to 1</div><div>That output was used to train snap. <br></div><div><br></div><div>Then I ran maker in "Gene prediction mode" as outlined on page 11 using the hmm file as input (and setting est2genome=0 and protein2genome=0). Repeat masking was enabled, again using my species specific library.</div><div><br></div><div>I trained snap for a second time.</div><div>That output was used as input for Basic Protocol 1 on page 3 of the aforementioned article.</div><div>Input for Basic Protocol 1 was:</div><div>The snap hmm file</div><div>my unmasked genome</div><div>the species specific repeat library</div><div>RNAseq evidence</div><div>the protein evidence from a close relative</div><div>softmasking was set to 1</div><div>est2genome=0</div><div>protein2genome=0</div><div><br></div><div>I collected the results as outlined on page 5 of the article.</div><div>However I noticed that there were no Fasta files.</div><div>Do you have any idea what could have gone wrong?</div><div>Can I send my log files to you? Thanks in advance for any assistance.</div><div><br></div><div>Kind Regards</div><div>Anna Yssel</div><div><br></div>
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</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div>Kind Regards<div>A Yssel</div><div><br></div><div><span style="color:rgb(34,34,34);font-family:Arial,sans-serif;font-size:12px;line-height:16px;text-align:-webkit-left;background-color:rgb(255,255,255)">Centre of Microbial and Plant Genetics</span><br style="vertical-align:top;color:rgb(34,34,34);font-family:Arial,sans-serif;font-size:12px;line-height:16px;text-align:-webkit-left;background-color:rgb(255,255,255)"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif;font-size:12px;line-height:16px;text-align:-webkit-left;background-color:rgb(255,255,255)">KU Leuven</span><br style="vertical-align:top;color:rgb(34,34,34);font-family:Arial,sans-serif;font-size:12px;line-height:16px;text-align:-webkit-left;background-color:rgb(255,255,255)"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif;font-size:12px;line-height:16px;text-align:-webkit-left;background-color:rgb(255,255,255)">Faculteit Bio-ingenieurswetenschappen </span><br style="vertical-align:top;color:rgb(34,34,34);font-family:Arial,sans-serif;font-size:12px;line-height:16px;text-align:-webkit-left;background-color:rgb(255,255,255)"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif;font-size:12px;line-height:16px;text-align:-webkit-left;background-color:rgb(255,255,255)">Kasteelpark Arenberg 20, bus 2460 </span><br style="vertical-align:top;color:rgb(34,34,34);font-family:Arial,sans-serif;font-size:12px;line-height:16px;text-align:-webkit-left;background-color:rgb(255,255,255)"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif;font-size:12px;line-height:16px;text-align:-webkit-left;background-color:rgb(255,255,255)">B-3001 Heverlee</span><br style="vertical-align:top;color:rgb(34,34,34);font-family:Arial,sans-serif;font-size:12px;line-height:16px;text-align:-webkit-left;background-color:rgb(255,255,255)"><span style="color:rgb(34,34,34);font-family:Arial,sans-serif;font-size:12px;line-height:16px;text-align:-webkit-left;background-color:rgb(255,255,255)">Belgium</span>
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