Hi Devon,
Thank you very much for your answer!
I agreed that these reads have a right insert size (the ones not are the 65
and 129), but I thought that 67/131 reads have the wrong orientation (both
reads are mapped to the forward strand in this case). To my understanding,
only the reads with flags of 99/147 or 83/163 are those properly paired
(with right insert size and orientation). Please correct me if I am wrong!
Thank you very much!
Best,
Xiao
2015-02-09 10:39 GMT-08:00 Devon Ryan <dpr...@dpryan.com>:
> Hi Xiao,
>
> Those flags explicitly indicate that the alignments are properly paired.
> The non-properly paired versions of those would be 65 and 129. You may find
> the "Explain SAM flags" page useful:
> https://broadinstitute.github.io/picard/explain-flags.html
>
> Best,
> Devon
>
> --
> Devon Ryan, Ph.D.
> Email: dpr...@dpryan.com
> Laboratory for Molecular and Cellular Cognition
> German Centre for Neurodegenerative Diseases (DZNE)
> Ludwig-Erhard-Allee 2
> 53175 Bonn
> Germany
> <devon.r...@dzne.de>
>
> On Mon, Feb 9, 2015 at 7:08 PM, Xiao Li <lixia...@gmail.com> wrote:
>
>> Dear samtools developer,
>>
>> Thank you for developing samtools! It is a very useful tool for my
>> research!
>>
>> I just have a quick question relevant to flagstat and it is very likely
>> that I misunderstood something. I realized that it actually classifies
>> reads with flag 67 and 131 as the "properly paired" reads in the report.
>> However, my understanding is that they are the reads mapped within the
>> insert size but wrong orientation. Did I misunderstood something here or
>> used the wrong command (I used samtools flagstat input-bam-file >
>> output-report) ? Thank you very much for your help!
>>
>> Best,
>>
>> Xiao
>>
>>
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