I have four sets of SOLiD NGS reads that are technical replicates of the same biological sample. My instinct is to map the reads separately for each replicate and then combine them for downstream analyses.
However, does anyone know whether it makes any difference combining the reads pre- or post-mapping?
The only thing i can think might be a problem about the former is that read ids might be replicated...
Normally we wouldn't have technical replicates, but this was done during a trial run of the bar-coding work-flow on a SOLiD 4 machine.