@maubp: those links were really helpful and cleared up my concerns! I had read an isoltated report and heard tell of the scary "B" but really didn't know what to make of it. Good thing I looked into it, because I was about to trim my Sanger-format FASTQ file that way, which would have been silly... Going back to re-trim from the Illumina format file!
@drio: good point! I'll try that and let you know how it goes. I guess I was just concerned about figuring out the best way to throw out the "bad quality" reads. I think armed with my new knowledge, I'll try some quality trimming and then run the test you suggest. Will post once the data is chewed
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