<div dir="ltr">Hi,<br><br>I just wanted to say thanks for all your help- I did the reciprocal best blast hits and then used the maker scripts (map_fasta_ids, map_gff_ids) to associate names between strain assemblies/annotations. Worked perfectly! -Janna<br>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Mar 14, 2014 at 11:02 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@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"><div><font face="Tahoma"><span style="font-size:13px">maker_map_ids does a translation (i.e. change gene-A to smug1), so you need to know which genes you want to translate names to (two column input file, column 1 -> original ID, column 2 -> new ID). I’m not sure EST forward is the best way to do this, although I do think </span></font><span style="font-family:Tahoma;font-size:13px">maker_map_ids is the tool to use in the end. The question is how to make a list of IDs to translate as the input to </span><span style="font-family:Tahoma;font-size:13px">maker_map_ids?</span></div>
<div><span style="font-family:Tahoma;font-size:13px"><br></span></div><div><font face="Tahoma"><span style="font-size:13px">I would actually just use BLASTP against the reference strain, and then do reciprocal best BLAST hits. To do this you BLAST your reference proteins against your maker proteins. Then do the opposite, BLAST your maker proteins against your reference proteins. If they are both each others best hit, then they are orthologous, and you can safely make a two column entry for the maker_map_ids input (i.e. maker-gene-1 translates into smug1).</span></font></div>
<div><font face="Tahoma"><span style="font-size:13px"><br></span></font></div><div><font face="Tahoma"><span style="font-size:13px">—Carson</span></font></div><div><font face="Tahoma"><span style="font-size:13px"><br></span></font></div>
<div style="font-size:14px;font-family:Calibri,sans-serif"><br></div><span style="font-size:14px;font-family:Calibri,sans-serif"><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span> Daniel Ence <<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>><br><span style="font-weight:bold">Date: </span> Friday, March 14, 2014 at 11:32 AM<br>
<span style="font-weight:bold">To: </span> Janna Fierst <<a href="mailto:jfierst@uoregon.edu" target="_blank">jfierst@uoregon.edu</a>>, "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span> Re: [maker-devel] associating gene names between related strains<br></div><div><div class="h5"><div><br></div><div dir="ltr"><div><div style="direction:ltr;font-size:10pt;font-family:Tahoma">
Hi Janna, So do you have one strain that you want to use as the reference for all the others? There's a script that comes with MAKER called maker_map_ids that lets you use a common
prefix or suffix for entries in a fasta file from one strain and then use est_forward to use that ID in the gene models for the other species.
<div><br></div><div>Let me know if that's not what you're looking for, </div><div>Daniel</div><div><div><br><div><font><div>Daniel Ence<br>
Graduate Student<br>
Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330</div></font></div></div><div style="font-size:16px;font-family:Times New Roman"><hr><div style="direction:ltr"><font color="#000000" face="Tahoma"><b>From:</b> maker-devel [<a href="mailto:maker-devel-bounces@yandell-lab.org" target="_blank">maker-devel-bounces@yandell-lab.org</a>] on behalf of Janna Fierst [<a href="mailto:jfierst@uoregon.edu" target="_blank">jfierst@uoregon.edu</a>]<br>
<b>Sent:</b> Friday, March 14, 2014 10:06 AM<br><b>To:</b> <a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a><br><b>Subject:</b> [maker-devel] associating gene names between related strains<br>
</font><br></div><div></div><div><div dir="ltr">Hi,<br><br>
we are assembling and annotating genomes for several related strains of Caenorhabditis worms and I was wondering if there is a way to coordinate the gene naming so that orthologs between species can be associated by name. I have been playing around a little
with the est_forward option but can't figure out a good system/workflow that preserves names but still uses the strain-specific RNA-Seq EST set for the actual gene models. Thanks! -Janna<br></div></div></div></div></div>
</div></div></div></div>
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