Question

Properly paired sequences ?

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5.6 years ago

pinn ▴ 210

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 • 1.6k views

ADD COMMENT • link updated 5.6 years ago by h.mon 35k • written 5.6 years ago by pinn ▴ 210

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calculating properly paired sequences doesn't differ from one to other tool?

yes: Tophat : Sam-Flag 115 = Properly-Paired + Read.Reverse + Mate.Reverse ? (old post)

ADD REPLY • link 5.6 years ago by Pierre Lindenbaum 161k

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

ADD REPLY • link 5.6 years ago by pinn ▴ 210

score 1 · Answer 1 · 2018-09-23

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5.6 years ago

h.mon 35k

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.

ADD COMMENT • link 5.6 years ago by h.mon 35k

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![I totally agree, follow the link https://ibb.co/gTGx99

ADD REPLY • link 5.6 years ago by pinn ▴ 210

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See: How to add images to a Biostars post

ADD REPLY • link 5.6 years ago by Ram 43k