this is my fist ChIP Seq analysis ever so I need some guidance from the more experienced ones.
I am now at the step of peak calling and decided to use MACS2 for this. My question is: if my control is SE but my treated samples are PE how should I handle this? Is this a problem? I think, that using only one strand for the PE is not a good idea.
You should be able to run both files using --format BAM, MACS2 should just use the 5' read of each pair in the PE file. As a SE analysis the fragment length will be calculated by cross correlation, however if you run MACS2 with the PE ChIP on its own then you can get the value 'd' from the log info. Then, when you run the SE analysis with the control you can use --nomodel --extsize 'd' (as its integer value'.
Thank you for the detailed answer! :)