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Old 02-25-2011, 01:31 AM   #2
Location: Cambridge area, UK

Join Date: Jan 2010
Posts: 35

I guess you are wondering about the bitwise flag of the SAM file (second field)
read unmapped means that that read is not mapped. the aligner does not know where to put it
mate unmapped means that the mate read (in a paired end sequencing) is unmapped.

At least this is my understanding.

hope this helps
stefanoberri is offline   Reply With Quote