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Old 05-22-2017, 05:10 PM   #6
nucacidhunter
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Location: Iran

Join Date: Jan 2013
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I think your library has had more than usual amount of adapter-dimers which is not removed with one final clean up after PCR. The reasons could be:

1- Low quality of input RNA
2- Low quantity of input
3- Sub-optimal library prep

If you look at libraries profile you should see a small peak around 150-160 bp representing dimers. Number of over-represented adapters should correlate to the molar quantity of 150 bp peak in each library. As fkruger has mentioned they will not align to genome.
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