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Old 09-09-2010, 05:40 AM   #1
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Location: taiwan

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Default What are the unmapped reads

Hi All,

In a normal run, we have 85% pass filter, then probably 80% mappable reads. Any idea what the good quality un-mappable reads are??
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Old 09-09-2010, 06:18 AM   #2
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1. Overestimated base quality. The reads are bad in fact.
2. Some aligners apply filters before alignment (e.g. polyA).
3. Some aligners may drop reads with extremely high copy number
4. The reference genome is imperfect.
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