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rururara 02-24-2011 11:52 PM

mate unmapped and read unmapped

Can anyone here explain what is mate unmapped and read unmapped?

stefanoberri 02-25-2011 01:31 AM

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

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