I am working with Illumina libraries on Galaxy.org.
I have used clip to remove Illumina adapters from the data set, it removed "too shorts, adapter-only, and the N-reads", (it removed >90,000). Strangely, I found if I re-run clip, it pulls even more out (>10,000, mostly "too-shorts and adapter only). Why would re-running the same search find more? I assume that maybe the original processing crated some new targets in the output, but that seems like a heck of a lot.
I have used clip to remove Illumina adapters from the data set, it removed "too shorts, adapter-only, and the N-reads", (it removed >90,000). Strangely, I found if I re-run clip, it pulls even more out (>10,000, mostly "too-shorts and adapter only). Why would re-running the same search find more? I assume that maybe the original processing crated some new targets in the output, but that seems like a heck of a lot.