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Properly paired sequences ?

Hi

Does each aligner has different flag stat ?

I'm interested in properly paired sequences how it can be calculated ? (formula)

samtools flagstat shows properly paired sequences, calculating properly paired sequences doesn't differ from one to other tool?

genome assembly sequence alignment
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updated by h.mon h.mon • written by pinn pinn

Does this setting differ between the genome aligners ? Can i trust the samtools flag-stat statistic for properly paired sequences

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written by pinn pinn

1 answer

The SAM flags indicating properly paired reads are part of the SAM specifications, and do not differ between tools (at least, between tools correctly implementing them). However, what is considered as "correctly paired" reads may change between aligners, and even within some aligners, depending on parameters used.

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written by h.mon h.mon

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