Question: Question about sam flags.
1
gravatar for mangfu100
2.8 years ago by
mangfu100460
Korea, Republic Of
mangfu100460 wrote:


Hi there.

While I am studying the samtool flags, I saw site below and thought that it was very useful.

https://ppotato.wordpress.com/2010/08/25/samtool-bitwise-flag-paired-reads/

However, In this webpages, I can't figure out that why samtool flags 81,161,97,145,65,129,113,188 is wrong insert size?

I looked this site up several times, but I didn't  understand why all these samtool flags refer to wrong insert size.

Can you help me?

sequencing alignment next-gen • 871 views
ADD COMMENTlink modified 2.8 years ago by geek_y8.0k • written 2.8 years ago by mangfu100460
7
gravatar for John Marshall
2.8 years ago by
John Marshall1.1k
Glasgow, Scotland
John Marshall1.1k wrote:

These flag values have both ends mapped, but not properly paired. The properly-paired/aligned flag is described as

    each segment properly aligned according to the aligner

which is not enormously clear, but typically means that the reads are mapped with appropriate orientation and insert size such that they plausibly reflect the whole template having been "nicely" mapped as a whole to the reference.

So having both ends mapped but not properly paired means that they have been mapped with either implausible orientations or an implausible insert size.

ADD COMMENTlink written 2.8 years ago by John Marshall1.1k
2
gravatar for geek_y
2.8 years ago by
geek_y8.0k
Barcelona/London
geek_y8.0k wrote:

Better refer this site for sam file flag information, which is also claimed to be source for the PDF:

http://broadinstitute.github.io/picard/explain-flags.html

 

ADD COMMENTlink written 2.8 years ago by geek_y8.0k
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