I have rna-seq data for five tissue samples and I am planning to use these for gene prediction.
Should I align them all together in one step to the genome or each tissue separately and later merge the bams??
I think you can map everything at once. If you are worried that you might loose isoform information - you can also do it separately for each tissue and merge only at the end.
I had pretty good experience with GAWN for that type of analysis - check it out.