SRA files: can they be merged before unpacking?

[epigenereg]

Hello,

I have to process several SRA files (from short read archive) which correspond to replicate experiments. What's the proper way:

1) Merge several SRA files together, then unpack, then map.
2) unpack individual SRA files, merge them, then map.
3) unpack individual SRA files, map them individually, then merge.

?

[biocomputer]

What kind of experiments are they? Biological or technical replicates? For example, if it's RNA-seq you want to keep your biological replicates separate so you can provide replicates to the program measuring differential expression (eg. Cufflinks/Cuffdiff).