Hello! can someone please give an opinion: does that make sense to merge PE reads before a de novo RNA-seq assembly (say with Trinity)? Merging tools are quite fast (like USEARCH www.drive5.com/usearch/manual/merge_pair.html) and the amount of raw data is reduced drastically. Can merged data be suitable for further assembly in a “single-ends” mode, or am I missing some theory behind it?.. Seems like it may save a lot of computations.
Thanks in advance. Leo