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Old 08-24-2012, 12:16 PM   #15
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Location: USA

Join Date: Jan 2012
Posts: 8

Your low aligned yield rate could be caused by many things but you can frequently diagnose some of the problems by looking at the sequence of what doesn't align. If they are very rich in either As or Ts, it was probably a sequencing problem. If short on Gs, it probably means the formaldehyde killed the Cs so you can't see the Gs. If an excess of CTAGs or portions thereof (standard Helicos base order of addition), you didn't filter properly. You may be able to sort out other issues by looking for common features of non-aligning sequences. For example, do they align to other species or does the same sequence keep appearing?
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