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Old 12-04-2010, 01:46 AM   #2
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

All of the unusual profiles are the result of the overrepresented sequence in your library. Having the same sequence make up 33% of the library will affect the overall base composition, Kmer composition and overall GC content.

As you said, the quality looks OK so there's no technical problem with the sequencing. The duplication level plot will tell you whether your problem is a small number of isolated sequences, or a generally high level of duplication in your library.

What you do about this will largely depend on what the overrepresented sequence is. If it's a small RNA then it just means you original sample is really biased, but if it's something like an adapter or primer then you may be able to improve your sample prep to get rid of it in future runs.
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