Frequently Asked Questions

Training session: Filter, Plot and Explore Single-cell RNA-seq Data

Speaker: Wendi Bacon

Q: My Scanpy FindMarkers step is giving me an empty table

A: Try selecting: “Use programme defaults: Yes” and see if that fixes it (Thanks Filippos Zacharaopoulos for that!) [Tools have updated since the tutorial was written using versions 1.6.0, and this toggle works slightly differently now]

Q: On Scanpy PlotEmbed, the tool is failing

A: Try selecting “Use raw attributes if present: NO” (Thanks Filippos Zacharaopoulos for that!) [Tools have updated since the tutorial was written using versions 1.6.0, and this toggle works slightly differently now]

Q: On the Scanpy PlotEmbed step, my object doesn’t have Il2ra or Cd8b1 or Cd8a etc.

A: Check your Anndata object - it should be 7874 x 14832, i.e. 7874 cells x 14832 genes. Is it actually 2000 genes only (i.e. and therefore missing the above markers)? You may have selected to remove genes at the Scanpy FindVariableGenes step (last toggle, ‘Remove genes not marked as highly variable’ < Select NO.) (Most likely you did this correctly the first time, but later in investigating how many got marked as highly variable, may have run this tool again and removed the nonvariable ones. We’ve updated the text to more clearly prevent this, but you may have gotten caught out!)