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Old 02-24-2011, 11:52 PM   #1
rururara
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Location: montreal

Join Date: Jan 2011
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Default mate unmapped and read unmapped

Hi,

Can anyone here explain what is mate unmapped and read unmapped?
Thanks!
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Old 02-25-2011, 01:31 AM   #2
stefanoberri
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Location: Cambridge area, UK

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Default

Hi
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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