How to get the median of read distribution in a genomic region?

Question

[jajclement]

Hi,

I have reads aligned on my genome and a file of genomic regions (peaks from peakcalling). I have reads falling into each regions according to a certain distribution and I would like to get the median of this distribution for each region, that is the genomic position corresponding to the median.

Do you know if an existing tool can do this ? Or do you have an idea how to compute this?

Thanks

[jotan]

Median? Do you mean the centre of the peak? The position where most of your reads map within a peak?