Hi all. I have a plasmid into which I cloned a chemically-synthesized oligo pool. The oligos differ from one another by single nucleotides and hence the resulting plasmid is highly complex/diverse in this particular region (which just so happens to be a gene of interest). I PCR'd across this hypervariable segment and deep-sequenced the amplicon and am now scratching my head as to how I should analyze the data. Does anyone have any software suggestions? I guess I was thinking there might be a way to automate a grep command so it systematically searches the fastq file for the informative segment of each oligo sequence. Can provide more info if required. Thanks!!!