Maybe post the command you used (end of the BAM file header), and the
flagstat output ...
On Tue, Apr 18, 2017 at 11:46 AM, oscar.migue...@mdc-berlin.de <
oscar.migue...@mdc-berlin.de> wrote:
> Dear Samtools community,
>
> I have a problem with rmdup I hope you can help me. I am working with
> paired-end data (samtools 1.3.1), I sort my file and then after using rmdup
> I use flagstat to check the number or reads and I see that single reads
> were eliminated not only pairs, I did not add any other option. I could
> just use "fixmate" to continue but I do not understand what is happening.
> It might be also important to note that before doing this I use "fixmate"
> to check everything is paired properly.
>
> Regards
>
>
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--
Joseph Fass
Bioinformatics Data Analyst
UC Davis Genome Center - Bioinformatics Core
http://bioinformatics.ucdavis.edu/
jnf...@ucdavis.edu
phone ~ 530.752.2698
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