text: user4951: I am having a single cell RNA seq data from ~500 Cells. I do understand this number is very low for present day analysis tools like Seurat. So, I want to know what if one have a such a small number of cells which tool works best?
  Thanks
  
  user2675: You can perfectly use any of the single cell processing packages out there. Seurat, Monocle3, Scanpy, Kallisto, etc. Following some of the tutorials and vignettes will most likely help you figuring out how to proceed. 
  These packages provide useful functions to explore single cell data, process the data and each of them has a series of advanced features to address specific questions. You don't need 10k cells to look at number of gene/cell, transcript/cells, % mitochondrial genes, etc. You can perfectly normalize and standardize 500 cells and run PCA, and analyze the complexity that describes your data. 
  To address if 500 cells is enough for you pilot we need to know what question you want to address.
  The following tool for example gives some intuition on how many cells to sample if you wish to detect n-cells per cluster. 
  https://satijalab.org/howmanycells
  Hopes this helps
  
original_text: 4951: <p>I am having a single cell RNA seq data from ~500 Cells. I do understand this number is very low for present day analysis tools like Seurat. So, I want to know what if one have a such a small number of cells which tool works best?</p>
  
  <p>Thanks</p>
   2675: <p>You can perfectly use any of the single cell processing packages out there. Seurat, Monocle3, Scanpy, Kallisto, etc. Following some of the tutorials and vignettes will most likely help you figuring out how to proceed. </p>
  
  <p>These packages provide useful functions to explore single cell data, process the data and each of them has a series of advanced features to address specific questions. You don't need 10k cells to look at number of gene/cell, transcript/cells, % mitochondrial genes, etc. You can perfectly normalize and standardize 500 cells and run PCA, and analyze the complexity that describes your data. </p>
  
  <p>To address if 500 cells is enough for you pilot we need to know what question you want to address.
  The following tool for example gives some intuition on how many cells to sample if you wish to detect n-cells per cluster. </p>
  
  <p><a href="https://satijalab.org/howmanycells" rel="nofollow noreferrer">https://satijalab.org/howmanycells</a></p>
  
  <p>Hopes this helps</p>
  