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I have a question on the BWA alignment. As I read the manual, it was saying "when you have paired-end reads, use bwa sampe instead of bwa samse". Any suggestion here?
Thanks,
Ben
Thanks,
Ben
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Hi Ben,
whats your question exactly? Do you want to understand the difference between sampe and samse? -
Paired reads can be more accurately mapped when both are mapped at the same time, as there is more information available. And for generation of a sam file, sampe allows the flag bits indicating pairing to be set correctly, which would not be the case with samse.
That said, I don't think you should use either one. BWA mem has superseded bwa aln + sampe/samse in speed and accuracy, and regardless, I prefer BBMap anyway
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