text: user1771: I want to filter out ribosomal RNA from scRNA-seq data (downloaded from here). Is there a list of known ribosomal RNA?
  The only solution I found is SortMeRNA, however it works with raw sequencing data afaik, while I already have a matrix with transcript counts for each cell. I searched for a comprehensive list of rRNAs but I didn't find any.
  
  user77: The rRNA genes in that dataset are Rn45s and Rn4.5s.
  BTW, you have gene counts, not transcript counts.
  
  user2139: In the paper mentioned, we used the ScaleData function in Seurat to regress out the number of reads, Rn45s abundance, and percent ribosomal gene transcripts. Ribosomal genes were found with the regular expression ^Rp[sl][[:digit:]].
  tiss <- ScaleData(object = tiss, vars.to.regress = c("nReads", "percent.ribo","Rn45s"))
  
  Here's a fuller notebook, and we'll have a better organized repository soon.
  
original_text: 1771: <p>I want to filter out ribosomal RNA from scRNA-seq data (downloaded from <a href="https://figshare.com/projects/Tabula_Muris_Transcriptomic_characterization_of_20_organs_and_tissues_from_Mus_musculus_at_single_cell_resolution/27733" rel="nofollow noreferrer">here</a>). Is there a list of known ribosomal RNA?</p>
  
  <p>The only solution I found is <a href="http://bioinfo.lifl.fr/RNA/sortmerna/" rel="nofollow noreferrer">SortMeRNA</a>, however it works with raw sequencing data afaik, while I already have a matrix with transcript counts for each cell. I searched for a comprehensive list of rRNAs but I didn't find any.</p>
   77: <p>The rRNA genes in that dataset are <code>Rn45s</code> and <code>Rn4.5s</code>.</p>
  
  <p>BTW, you have gene counts, not transcript counts.</p>
   2139: <p>In the paper mentioned, we used the <code>ScaleData</code> function in Seurat to regress out the number of reads, Rn45s abundance, and percent ribosomal gene transcripts. Ribosomal genes were found with the regular expression <code>^Rp[sl][[:digit:]]</code>.</p>
  
  <pre><code>tiss &lt;- ScaleData(object = tiss, vars.to.regress = c("nReads", "percent.ribo","Rn45s"))
  </code></pre>
  
  <p><a href="https://github.com/czbiohub/maca/blob/master/MACA_Plate_Notebook.Rmd" rel="nofollow noreferrer">Here's</a> a fuller notebook, and we'll have a better organized repository soon.</p>
  