Chip-Seq Combining the Replicates
Hi,
I have two Chip-Seq samples obtained under the same conditions but experimented at two different times (one is last year and other one recently). I called the peaks using MACS. Peak coordinates were slighly different, but with a window size of 250 bp the peaks are reproducible in two sets.
To be more clear, how I calculated the final peaks from two sets is:
Rep1 : Chr13 : 15624330 - 15625274
Rep2 : Chr13 : 15624541 - 15625555
As the distance between two peak starts is < 250 ; I called the adjusted peak as
Chr13 : 15624330 - 15625555
What will be the optimal window size to set ?? Is window size of 250 is fine or should I increase to 350 or 450 ??
Any suggestions is warmly welcome
I have two Chip-Seq samples obtained under the same conditions but experimented at two different times (one is last year and other one recently). I called the peaks using MACS. Peak coordinates were slighly different, but with a window size of 250 bp the peaks are reproducible in two sets.
To be more clear, how I calculated the final peaks from two sets is:
Rep1 : Chr13 : 15624330 - 15625274
Rep2 : Chr13 : 15624541 - 15625555
As the distance between two peak starts is < 250 ; I called the adjusted peak as
Chr13 : 15624330 - 15625555
What will be the optimal window size to set ?? Is window size of 250 is fine or should I increase to 350 or 450 ??
Any suggestions is warmly welcome