How to calculate the Average Insert Size after mapping the reads to the reference genome using BWA
Having mapped the reads to the reference genome using BWA, I am trying to calculate their Average Insert Size.
Thereafter, I converted the BAM file to SAM file in order to check the ISIZE values.
Since these values are both positive and negative, when I calculate the average value (using Summary Statistics) the result is always zero.
Does anyone know any way to deal with these negative values?
many thanks in advance
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