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Has anyone used BWA with paired end reads where the reads overlap? I'm talking about reads that would result from running a 2x100 PE run where the size-selected fragment size is less than 200bp (so some parts of the fragment are sequenced twice).
I might have some reads coming off a machine soon and I was wondering if there were issues with the systemic computation of insert size (which is effectively a negative number). Actually I'm interested in hearing feedback from anyone who has aligned these kinds of reads with any aligner to see what kind of results I get with different methods.
I might have some reads coming off a machine soon and I was wondering if there were issues with the systemic computation of insert size (which is effectively a negative number). Actually I'm interested in hearing feedback from anyone who has aligned these kinds of reads with any aligner to see what kind of results I get with different methods.
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