Hi,
I am using BWA to align single reads to reference genome using BWA. Because the sequenced genome is quite diverged from the reference (genetic distance is about 40 to 50%, but still belong to the same species), I am curious how many reads are not aligned by BWA, how to find out this information?
Thanks
I am using BWA to align single reads to reference genome using BWA. Because the sequenced genome is quite diverged from the reference (genetic distance is about 40 to 50%, but still belong to the same species), I am curious how many reads are not aligned by BWA, how to find out this information?
Thanks
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