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install_organisms_FASTA_GTF.html
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<title>Installing genomes from FASTA and GTF files</title>
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<h1 class="title toc-ignore">Installing genomes from FASTA and GTF files</h1>
<h4 class="author">Bruno Contreras Moreira</h4>
<h4 class="date">2022-04-07</h4>
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<p>This protocol uses the Makefile <a href="https://github.com/rsa-tools/rsat-code/blob/master/makefiles/ensemblgenomes_FTP_client.mk">ensemblgenomes_FTP_client.mk</a>, which can also be used to install organisms from Ensembl Genomes, as explained in <a href="https://rsa-tools.github.io/managing-RSAT/genome_installation/install_organisms_ensembl_genomes.html">Installing genomes from Ensembl Genomes</a>.</p>
<p>This procedure supports the installation of arbitrary genomes from any sources, provided that 4 input files are obtained with the following extensions:</p>
<ul>
<li>$SPECIES_RSAT_ID.dna.toplevel.fa : raw genomic sequence</li>
<li>$SPECIES_RSAT_ID.dna_rm.genome.fa : repeat-hard-masked genomic sequence</li>
<li>$SPECIES_RSAT_ID.gtf : annotation file</li>
<li>$SPECIES_RSAT_ID.pep.all.fa : peptide sequences of CDS features</li>
</ul>
<p>where SPECIES_RSAT_ID is a string identifying this organism and its annotation.</p>
<p>Note: parse-gtf takes also GFF3 files, but the script expects the .gtf extension</p>
<p>For instance, to install assembly Wm82.a2.v1 of <em>Glycine max</em> from <a href="https://phytozome.jgi.doe.gov">JGI Phytozome</a>, we could do:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> <span class="va">$RSAT</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="va">SPECIES_RSAT_ID</span><span class="op">=</span>Glycine_max.Wm82.a2.v1.JGI</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> <span class="va">$RSAT</span>/data/genomes/<span class="va">${SPECIES_RSAT_ID}</span>/genome</span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="co"># put there those 4 files (dna.toplevel.fa,dna_rm.genome.fa,.gtf,.pep.all.fa)</span></span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="fu">make</span> <span class="at">-f</span> makefiles/ensemblgenomes_FTP_client.mk SPECIES=Glycine_max <span class="dt">\</span></span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a> SPECIES_DIR=/var/www/html/rsat/data/genomes/<span class="va">$SPECIES_RSAT_ID</span> <span class="dt">\</span></span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a> SPECIES_RSAT_ID=<span class="va">$SPECIES_RSAT_ID</span> TAXON_ID=3847 GTF_SOURCE=JGI <span class="dt">\</span></span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a> install_from_gtf</span></code></pre></div>
<p>Note that TAXON_ID can be obtained at <a href="https://www.ncbi.nlm.nih.gov/taxonomy" class="uri">https://www.ncbi.nlm.nih.gov/taxonomy</a></p>
<p>The newly installed species will be added to $RSAT/data/supported_organisms.tab and should be listed with the following command-line:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">supported-organisms</span></span></code></pre></div>
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