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Thread Tools |
08-22-2013, 07:25 PM
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#1 |
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Member
Location: Beijing Join Date: Nov 2012
Posts: 16
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why the properly paired results from bwa mem is an odd number
Hi
following is the results of samtools flagstat results. I use bwa mem default command to do align! my question is why the properly paired is odd number? 25700926 mapped 25744459 + paired in sequencing 12897523 read1 12846936 read2 25445603 properly paired 25692729 with itself and mate mapped 8197 singletons my reads are from a archaea RNA-seq experiment. and how to get unique mapped read-pairs from the properly paired? thanks! |
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08-23-2013, 10:42 AM
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#2 |
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Senior Member
Location: Boston Join Date: Feb 2008
Posts: 693
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That is because of chimeric alignment.
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08-24-2013, 07:26 PM
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#3 |
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Member
Location: Beijing Join Date: Nov 2012
Posts: 16
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Thanks for your reply!
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| odd number, properly paired |
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