How to calculate the Average Insert Size after mapping the reads to the reference genome using BWA

How to calculate the Average Insert Size after mapping the reads to the reference genome using BWA

3

Hi,

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


alignment

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