Using the cuffmerge to merge the ssRNASeq data and non-ssRNASeq data

[satp]

Hi everyone,

I have downloaded some strand-specific RNA-Seq data and non strand-specific RNA-Seq data from SRA, and assembled them using the cufflinks respectively. Can the assembled results of ssRNA-Seq data and non ssRNA-Seq be merged together using cuffmerge, or they must be merged separatedly?

Best,
Jian-You