Question: Properly paired sequences ?
0
gravatar for pinninti1991reddy
12 weeks 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 12 weeks ago by h.mon21k • written 12 weeks 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 12 weeks ago by Pierre Lindenbaum115k

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

ADD REPLYlink written 12 weeks ago by pinninti1991reddy30
1
gravatar for h.mon
12 weeks ago by
h.mon21k
Brazil
h.mon21k 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 12 weeks ago by h.mon21k

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

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by pinninti1991reddy30

See: How to add images to a Biostars post

ADD REPLYlink written 11 weeks ago by RamRS19k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 749 users visited in the last hour