Our pipeline runs the FastqScreen tool twice with 2 different databases. The first database contains all the organisms (human/mouse/bacteria/fungi) and the second database contains adapters/primers/ribosomal sequences etc. If reads from a sample do not “hit” anything in a particular database, then they are depicted as “no hit”. Unless your sequences are heavily laden with adapters, the alignment to the second database does typically show significant percentage of “no hits”. This is expected. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.
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