running multiple GEO Dataset projects

Question

[analyst]

My aim is to extract RNAseq counts and novel genes from 10 rice RNAseq datasets (online datasets GEO datasets) under drought condition only. Few are from leaf and few from seed tissue part. Can I put all samples from all datasets together in one folder and run RNAseq pipeline (hisat2 --> stringtie merge --> stringtie quant) or should I run each dataset separately.

Thanks for your guidance.