<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Sorry I meant to say prefilter on the score in the mRNA column before passing the gff3 to model_gff.</div><div><br></div><div>--Carson <br><br>Sent from my iPhone</div><div><br>On Feb 26, 2014, at 3:50 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div><div>What you can do is run it once with just est_forward=1 and est2genome/protein2genome set to 1. Then take those results, pass them in as model_gff and use the map_forward option to then filter the results based on mRNA score and that would copy names onto new gene under the standard MAKER pipeline. Eventually it’s really supposed to go into a separate tool that will map genes onto new assemblies (but under the hood the tool will just be calling MAKER with certain parameters restricted). I do this because if people commonly use it mixed with things like SNAP I can start to get some very weird behaviors. </div><div><br></div><div>Thanks,</div><div>Carson</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> Mikael Brandström Durling <<a href="mailto:mikael.durling@slu.se">mikael.durling@slu.se</a>><br><span style="font-weight:bold">Date: </span> Wednesday, February 26, 2014 at 3:04 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </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> Re: [maker-devel] Mapping gene names<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html; charset=Windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
It seems that this could be a very useful option in those cases where you have firm a priori knowledge of the placement of ESTs. However, while trying it I note that est_forward implies that the est2genome predictor is turned on, implicitly. Is this necessary
for this to work? I’m after the behavior you describe below where exonerate is made to try really hard within a limited region to align an est, but I would not like maker to produce est2genome predictions.
<div><br></div><div>In general, I think this maker_coor and est_forward is a feature set that is worthy to be promoted into a documented feature.</div><div><br></div><div>THanks,</div><div>Mikael</div><div><br><div><div>26 feb 2014 kl. 17:09 skrev Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 14px; font-family: Calibri, sans-serif;"><div>It will still work without est_forward. It just works a little differently. Keep in mind this was a hidden feature I used to find stubborn or hard to find missing genes after reassembly of a genome.</div><div><br></div><div>If est_forward is provided, MAKER will parse the database to look for the maker_coor tags early in the pipeline. Then it will create a list of locations to search, and it will search them even if there are no BLAST results to seed the search (normally
MAKER gets a BLAST result first and then polishes it with exonerate). So maker_coor=chr1 will cause MAKER to look for a match using all of chr1 as the input to exonerate even when BLAST finds nothing (this is a very very slow search, but can help pick up
one or two stubborn genes that don’t remap well). To allow this, MAKER gives exonerate looser matching parameters (i.e. allows for single base pair introns perhaps caused by assembly errors). The logic here is that given the fact that I already told MAKER
that with some degree of confidence I expect sequence A to map to to location X, it will try its hardest to make it match. </div><div><br></div><div>Without est_forward set, the maker_coor= flag still gets read in GI.pm at line 1563, but only after a BLAST alignment has already seeded it to the region (that BLAST result has the information in its description parameter). MAKER will then ignore seeds
completely outside of maker_coor. In addition any BLAST seeds that overlap maker_coor will get the search space for alignment polishing adjusted to match maker_coor exactly. Also match parameters for exonerate will not be relaxed as they were with est_forward.</div><div><br></div><div>As you can see the behavior, is slightly different (because it’s an accidental feature).</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family: Calibri; font-size: 11pt; text-align: left; border-width: 1pt medium medium; border-style: solid none none; padding: 3pt 0in 0in; border-top-color: rgb(181, 196, 223);"><span style="font-weight:bold">From: </span>Mikael Brandström Durling <<a href="mailto:mikael.durling@slu.se">mikael.durling@slu.se</a>><br><span style="font-weight:bold">Date: </span>Wednesday, February 26, 2014 at 6:37 AM<br><span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </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>Re: [maker-devel] Mapping gene names<br></div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
That might be a useful and time saving accidental feature. But, reading the code, it seems that I need to supply maker_coor but not gene_id, as well as the configuration option est_forward for this to work. Any occurrences of maker_coor in GI.pm seems to be
conditioned on set_forward=1 right?
<div><br></div><div>Mikael</div><div><br><div><div>26 feb 2014 kl. 14:22 skrev Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="auto"><div>Yes. That should work as well as an accidental feature.</div><div><br></div><div>--Carson <br><br>
Sent from my iPhone</div><div><br>
On Feb 26, 2014, at 5:30 AM, Mikael Brandström Durling <<a href="mailto:mikael.durling@slu.se">mikael.durling@slu.se</a>> wrote:<br><br></div><blockquote type="cite">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?
<div><br></div><div>Thanks,</div><div>Mikael</div><div><br><div><div>26 feb 2014 kl. 01:58 skrev Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 14px; font-family: Calibri, sans-serif;"><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><div><br></div><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><div><br></div><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><div><br></div><div>—Carson</div><div><br></div><div><br></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family: Calibri; font-size: 11pt; text-align: left; border-width: 1pt medium medium; border-style: solid none none; padding: 3pt 0in 0in; border-top-color: rgb(181, 196, 223);"><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></div><div><br></div><div dir="ltr"><div class="markdown-here-wrapper" id="markdown-here-wrapper-435708" style=""><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></div></div>
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