merging bam file

Question

[qudrat.nii]

Hello everyone!

I have done two independent chipseq for a transcription factor with two replicate in each experiment. I want to merge the bam file of replicates but I do not know what condition is required for merging bam file. Every replicate file has different sequencing depth and their alignment is also not similar. What is exact condition when bam files can be merged? Any leads would be appreciated.

[biofalconch]

You can check if your samples look like replicates or independant samples by checking correlation using deeptools:

https://deeptools.readthedocs.io/en/develop/content/tools/plotCorrelation.html