Psuedobulk analysis of single cell RNA-Seq data

Question

[evocanres]

I have a single cell RNA Seq dataset from Fluidigm C1 Chip. Given that I have 50+ and 30+ cells in two groups respectively, would it be okay, to merge the Fastq files of each groups and do a pseudo-bulk analysis ?

[Trivas]

If I understand you right, this would turn your data into N=1 for each group. Possible to do a hacky DGE but not a well designed one.

[evocanres]

trivial as it may sound, how about making N=3 for each group ?

[Nitin Narwade]

Actually, you can, by random subsampling.

Nice tutorial from Fabian Theis could be of great help.

Cheers!!

Nitin N.