text: user208: We have RNA-seq data from libraries prepared using the Smartseq2 single-cell protocol on 500 cells (mini-bulk) / library. The complexity is much better than with single-cells (~14k genes for 1.5M reads).
  6 cell types / biological replicates were collected with flow cytometry, and there are 4 control and 5 diseased biological replicates (patients).
  We are mostly interested in the differences between control and disease either overall or within each cell type.
  Can single-cell tools (e.g. Seurat) be used on this dataset? It is neither bulk nor single-cell data. How would you approach this? 
  
  user35: Single-cell tools were developed to address some specific factors unique to scRNA-seq, such as:
  
  a lot of dropouts, so hundreds or thousands of detected genes, not tens of thousands (for mammalian genomes)
  hundreds or thousands of replicates
  not necessarily well-defined groups
  
  Thus, I would say your experiment is a lot closer to bulk RNA-seq than scRNA-seq.
  
original_text: 208: <p>We have RNA-seq data from libraries prepared using the Smartseq2 single-cell protocol on <strong>500 cells</strong> (mini-bulk) / library. The complexity is much better than with single-cells (~14k genes for 1.5M reads).</p>
  
  <p>6 cell types / biological replicates were collected with flow cytometry, and there are 4 control and 5 diseased biological replicates (patients).</p>
  
  <p>We are mostly interested in the differences between control and disease either overall or within each cell type.</p>
  
  <p>Can single-cell tools (e.g. Seurat) be used on this dataset? It is neither bulk nor single-cell data. How would you approach this? </p>
   35: <p>Single-cell tools were developed to address some specific factors unique to scRNA-seq, such as:</p>
  
  <ul>
  <li>a lot of dropouts, so hundreds or thousands of detected genes, not tens of thousands (for mammalian genomes)</li>
  <li>hundreds or thousands of replicates</li>
  <li>not necessarily well-defined groups</li>
  </ul>
  
  <p>Thus, I would say your experiment is a lot closer to bulk RNA-seq than scRNA-seq.</p>
  