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Hello All,
I am relatively new to using BWA, and I am hoping to better understand the maximum edit distance parameter, -n. The manual says that when n is expressed as a decimal it is "the fraction of missing alignments given 2% uniform base error rate". What does this mean?
I have tried using a -n value of 0.04, 0.03, 0.02 and 0.01 and found that 0.01 returns the largest number of high quality reads that aligned to my reference.
I would like to understand the meaning of what I am doing when I change this parameter. Am making the criteria for alignment more and more stringent as I use a lower number? If so, why should I get more reads aligning to the reference?
Thanks so much for your help!
Jessie
I am relatively new to using BWA, and I am hoping to better understand the maximum edit distance parameter, -n. The manual says that when n is expressed as a decimal it is "the fraction of missing alignments given 2% uniform base error rate". What does this mean?
I have tried using a -n value of 0.04, 0.03, 0.02 and 0.01 and found that 0.01 returns the largest number of high quality reads that aligned to my reference.
I would like to understand the meaning of what I am doing when I change this parameter. Am making the criteria for alignment more and more stringent as I use a lower number? If so, why should I get more reads aligning to the reference?
Thanks so much for your help!
Jessie