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Old 08-09-2011, 10:07 AM   #1
fabrice
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Default From sam file, how to the mate aligned or not?

For paired-end data, which flag to indicate the mate aligned or not?

Thanks.
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Old 08-09-2011, 10:17 AM   #2
swbarnes2
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If the 8 flag is set, the mate didn't map. It's right there in the .sam format description.
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Old 08-09-2011, 10:37 AM   #3
fabrice
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PNEXT: Position of the NEXT fragment in the template. Set as 0 when the information is
unavailable. This eld equals POS of the next fragment. If PNEXT is 0, no assumptions can be
made on RNEXT and bit 0x20.

If the 8 flag is set, the mate map?

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Originally Posted by swbarnes2 View Post
If the 8 flag is set, the mate didn't map. It's right there in the .sam format description.
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