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Can this use of maker_coor be used only to hint about the placement of the ests, without affecting the naming of the final genes? Ie if I have a database of EST where I have a priori knowledge of their rough placement, can this placement be given to maker without
providing est_forward=1?
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<div>Thanks,</div>
<div>Mikael</div>
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<div>26 feb 2014 kl. 01:58 skrev Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>:</div>
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<div>There is a way. It’s not a standard option and it’s undocumented, but if you add est_forward=1 to the maker_opts.ctl file, then it will do just that. The option won’t already be there so you’ll have to type it in.</div>
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<div>There is also a feature designed to work with this option. If you add tags to your fasta headers, those can be used to guide the mapping and naming. For example, gene_id=<some_gene> will ensure different isoforms that share a common gene_id get clustered
into the same gene, and maker_coor=chr1:1-10000 in the fasta header will force a particular sequence to only be mapped against chr1 within the range of 1-10000 bp and just using maker_coor=chr1 will force it to only be mapped against chr1.</div>
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<div>This is an undocumented way to remap genes onto new assemblies using blast alignments of earlier transcript or protein annotations as a guide.</div>
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<div>—Carson</div>
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<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">Reply-To: </span>Shaun Jackman <<a href="mailto:sjackman@gmail.com">sjackman@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, February 25, 2014 at 5:06 PM<br>
<span style="font-weight:bold">To: </span><<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>[maker-devel] Mapping gene names<br>
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<p style="margin:1.2em 0px!important">Hi,</p>
<p style="margin:1.2em 0px!important">I’m annotating a genome using a closely related genome from Genbank, using the .frn (RNA) and .faa (protein) files from Genbank as evidence to annotate my genome. I’ve run Maker, and the annotation seems to have worked
well. Is it possible to map the names of the genes from the related species to my annotation? I see the
<em>map_forward</em> option, which applies to the <em>model_gff</em> parameter. Is there a similar option for
<em>est</em> and <em>protein</em>?</p>
<p style="margin:1.2em 0px!important"><em>maker_opts.ctl</em></p>
<pre style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;margin:1.2em 0px"><code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline;white-space:pre;overflow:auto;border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;border:1px solid rgb(204,204,204);padding:0.5em 0.7em;display:block!important;display:block;padding:0.5em;color:rgb(51,51,51);background-color:rgb(248,248,255);background-repeat:initial initial">est=NC_123456.frn
protein=NC_123456.faa
est2genome=1
protein2genome=1
</code></pre>
<p style="margin:1.2em 0px!important">Thanks,<br>
Shaun</p>
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