What are the unmapped reads

beelu · 09-09-2010, 05:40 AM

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??

lh3 · 09-09-2010, 06:18 AM

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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09-09-2010, 05:40 AM	#1
beelu Junior Member Location: taiwan Join Date: Mar 2008 Posts: 7	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??

09-09-2010, 06:18 AM	#2
lh3 Senior Member Location: Boston Join Date: Feb 2008 Posts: 693	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.