Question: Properly paired sequences ?
0
gravatar for pinninti1991reddy
4 months ago by
pinninti1991reddy30 wrote:

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?

ADD COMMENTlink modified 4 months ago by h.mon23k • written 4 months ago by pinninti1991reddy30
1

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 REPLYlink written 4 months ago by Pierre Lindenbaum116k

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

ADD REPLYlink written 4 months ago by pinninti1991reddy30
1
gravatar for h.mon
4 months ago by
h.mon23k
Brazil
h.mon23k wrote:

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 COMMENTlink written 4 months ago by h.mon23k

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

ADD REPLYlink modified 4 months ago • written 4 months ago by pinninti1991reddy30

See: How to add images to a Biostars post

ADD REPLYlink written 4 months ago by RamRS20k
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