<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>Whichever has the best AED score I believe, but you can add gene_id= to the header of each fasta file to ensure MAKER doesn't try and cluster unrelated transcripts into a single gene. Then the transcript name and gene name will be guaranteed to match up.</div><div><br></div><div>--Carson</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> Shaun Jackman <<a href="mailto:sjackman@gmail.com">sjackman@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Wednesday, April 30, 2014 at 5:25 PM<br><span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] est_forward and conflicting names<br></div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><p>Hi, Carson.</p><p>I’ve downloaded a number genes from GenBank using Entrez Direct, which I’m using with <code>est</code> and <code>protein</code> to annotate a plant mitochondrion. Most of these reference sequences have sensible and consistent gene names, and so I’m using <code>est_forward</code> to retain the gene names. This workflow is working well for me. Some of the genes pulled in from GenBank have less useful names like <code>orf1234</code> or other numeric IDs. When multiple evidence sequences map to the same location, how does <code>est_forward</code> choose which name to use? If it’s chosen arbitrarily, could it be possible to choose the most common name instead?</p><p>Thanks,<br>
Shaun</p><p><style>body{font-family:Helvetica,Arial;font-size:13px}</style><style>body {
font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
padding:1em;
margin:auto;
background:#fefefe;
}
h1, h2, h3, h4, h5, h6 {
font-weight: bold;
}
h1 {
color: #000000;
font-size: 28pt;
}
h2 {
border-bottom: 1px solid #CCCCCC;
color: #000000;
font-size: 24px;
}
h3 {
font-size: 18px;
}
h4 {
font-size: 16px;
}
h5 {
font-size: 14px;
}
h6 {
color: #777777;
background-color: inherit;
font-size: 14px;
}
hr {
height: 0.2em;
border: 0;
color: #CCCCCC;
background-color: #CCCCCC;
}
p, blockquote, ul, ol, dl, li, table, pre {
margin: 15px 0;
}
a, a:visited {
color: #4183C4;
background-color: inherit;
text-decoration: none;
}
#message {
border-radius: 6px;
border: 1px solid #ccc;
display:block;
width:100%;
height:60px;
margin:6px 0px;
}
button, #ws {
font-size: 12 pt;
padding: 4px 6px;
border-radius: 5px;
border: 1px solid #bbb;
background-color: #eee;
}
code, pre, #ws, #message {
font-family: Monaco;
font-size: 10pt;
border-radius: 3px;
background-color: #F8F8F8;
color: inherit;
}
code {
border: 1px solid #EAEAEA;
margin: 0 2px;
padding: 0 5px;
}
pre {
border: 1px solid #CCCCCC;
overflow: auto;
padding: 4px 8px;
}
pre > code {
border: 0;
margin: 0;
padding: 0;
}
#ws { background-color: #f8f8f8; }
table {
border-collapse: collapse;
font-family: Helvetica, arial, freesans, clean, sans-serif;
color: rgb(51, 51, 51);
font-size: 15px; line-height: 25px;
padding: 0; }
table tr {
border-top: 1px solid #cccccc;
background-color: white;
margin: 0;
padding: 0; }
table tr:nth-child(2n) {
background-color: #f8f8f8; }
table tr th {
font-weight: bold;
border: 1px solid #cccccc;
margin: 0;
padding: 6px 13px; }
table tr td {
border: 1px solid #cccccc;
margin: 0;
padding: 6px 13px; }
table tr th :first-child, table tr td :first-child {
margin-top: 0; }
table tr th :last-child, table tr td :last-child {
margin-bottom: 0; }
.send { color:#77bb77; }
.server { color:#7799bb; }
.error { color:#AA0000; }</style></p><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><p></p></div></div>_______________________________________________
maker-devel mailing list
<a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a>
</span></body></html>