This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Cellranger counts: how to set the value for "--expect-cells" if you can't guess

I see "cellranger counts" recommends people estimate the number of cells in the samples they want to analyze (with the "--expect-cells" argument, and it has a default value of 3000 cells if you don't input a value) - if I don't know how many cells are in my sample and I couldn't make a good guess, is there any good guidance for what to do then? I haven't seen any questions on Biostars or elsewhere about this in particular.

Cellranger counts: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count#cr-count

cellranger-counts cellranger
• 3,881 views • link
written by Aaron • Aaron

You can start with the default and see what you get. If you had counted the number of cells that went into the experiment then you could try that number.

• 0 views • link
written by GenoMax GenoMax

Thanks GenoMax this is very helpful. Unfortunately, I'm using data collected by someone else and I can't seem to find any record of cells counted - is there a way to estimate the number of cells if they weren't initially counted?

• 0 views • link
written by Aaron • Aaron

1 answer

Generally speaking, using 3000 or 5000 won't generate too much difference. But 300 and 5000 may lead to significantly different result. Cellranger just use this value as a rough range for its algorithm. The final cell number is determined by the "knee plot".

• 0 views • link
written by shiyang_bio • shiyang_bio

This is very helpful @shiyang_bio, thank you!

• 0 views • link
written by Aaron • Aaron

Log in to answer this question.

More posts like this