Issue with gene names in simulated data

[martina811]

Hi!
I’m currently using a real scRNA-seq reference dataset as input to simuRNAseq, and I noticed that the gene names (rownames) in the simulated counts matrix (dat$counts) do not match the gene names in my original reference panel (input counts matrix).

Would it be possible to clarify:

• Why gene names are randomized or replaced in the output?
• Whether there is a way to retain the original gene identifiers from the input panel?

This would be very helpful for realistic benchmarking scenarios where preserving gene identity is important.

Thank you!

[ChangjiangXu]

The original gene names will be retained if the number of simulated genes is equal to the number of the genes in the reference data. Otherwise, the genes will be randomly selected or generated.