text: user1075: Where can I find the DNA sequence of the C. elegans rRNA cluster?
  Ideally, I would be able to do it using the command-line.
  I've tried using NCBI but the results are unsatisfactory. I am interested in the DNA sequence that is in the current reference genome of WormBase.
  I have tried using the Bioconductor biomaRt package and create a table containing the description but when I grep 'rRNA', I only get proteins doing things with rRNA. I used the following code:
  ensembl <- biomaRt::useMart('ensembl', dataset = 'celegans_gene_ensembl')
  wormGenes <- biomaRt::getBM(attributes = c('external_gene_name', 'chromosome_name', 'start_position', 'end_position', 'gene_biotype', 'description'), mart = ensembl)
  wormGenes[grep('rRNA', wormGenes$description), 6]
  
  [1] "rRNA 2'-O-methyltransferase fibrillarin  [Source:UniProtKB/Swiss-Prot;Acc:Q22053]"      
  [2] "Pre-rRNA-processing protein pro-1  [Source:UniProtKB/Swiss-Prot;Acc:Q22006]"            
  [3] "Pre-rRNA-processing protein TSR1 homolog  [Source:UniProtKB/Swiss-Prot;Acc:Q19329]"     
  [4] "rRNA methyltransferase 2, mitochondrial  [Source:UniProtKB/Swiss-Prot;Acc:O62251]"      
  [5] "Probable rRNA-processing protein EBP2 homolog  [Source:UniProtKB/Swiss-Prot;Acc:Q09958]"
  [6] "Putative rRNA methyltransferase  [Source:UniProtKB/TrEMBL;Acc:Q5CCJ2]" 
  
  
  user1075: The info is actually in the gene_biotype column of my wormGenes data frame. I could select the rRNA genes using dplyr::filter(wormGenes, gene_biotype == 'rRNA'). Unfortunately, no description is available for the genes, so I will have to get it using the gene IDs.
  
original_text: 1075: <p>Where can I find the DNA sequence of the <em>C. elegans</em> rRNA cluster?</p>
  
  <p>Ideally, I would be able to do it using the command-line.</p>
  
  <p>I've tried using <a href="https://www.ncbi.nlm.nih.gov/nuccore/?term=ribosomal%20RNA%20caenorhabditis%20elegans" rel="nofollow noreferrer">NCBI</a> but the results are unsatisfactory. I am interested in the DNA sequence that is in the current reference genome of <a href="http://wormbase.org/" rel="nofollow noreferrer">WormBase</a>.</p>
  
  <p>I have tried using the Bioconductor biomaRt package and create a table containing the description but when I grep 'rRNA', I only get proteins doing things with rRNA. I used the following code:</p>
  
  <pre><code>ensembl &lt;- biomaRt::useMart('ensembl', dataset = 'celegans_gene_ensembl')
  wormGenes &lt;- biomaRt::getBM(attributes = c('external_gene_name', 'chromosome_name', 'start_position', 'end_position', 'gene_biotype', 'description'), mart = ensembl)
  wormGenes[grep('rRNA', wormGenes$description), 6]
  
  [1] "rRNA 2'-O-methyltransferase fibrillarin  [Source:UniProtKB/Swiss-Prot;Acc:Q22053]"      
  [2] "Pre-rRNA-processing protein pro-1  [Source:UniProtKB/Swiss-Prot;Acc:Q22006]"            
  [3] "Pre-rRNA-processing protein TSR1 homolog  [Source:UniProtKB/Swiss-Prot;Acc:Q19329]"     
  [4] "rRNA methyltransferase 2, mitochondrial  [Source:UniProtKB/Swiss-Prot;Acc:O62251]"      
  [5] "Probable rRNA-processing protein EBP2 homolog  [Source:UniProtKB/Swiss-Prot;Acc:Q09958]"
  [6] "Putative rRNA methyltransferase  [Source:UniProtKB/TrEMBL;Acc:Q5CCJ2]" 
  </code></pre>
   1075: <p>The info is actually in the <code>gene_biotype</code> column of my <code>wormGenes</code> data frame. I could select the rRNA genes using <code>dplyr::filter(wormGenes, gene_biotype == 'rRNA')</code>. Unfortunately, no description is available for the genes, so I will have to get it using the gene IDs.</p>
  