Question: How are multiple replicates of control condition used? about cutandrun

[code-flowbio]

Hi Christoph thanks for your quesiton. In my experience of CUT&RUN, biological replicates are often paired together with their controls therefore that is the default. You are correct that if there is a mismatch of replicates only the first is used. If you want a single control from multiple control samples, then indeed you need to set them as technical replicates and they will automatically be merged by setting the same sample id and replicate number.

[ChristophH]

@code-flowbio Thank you for your reply. Our experimental setup did not allow for paired control non-control samples. I ended up merging the control samples as suggested above.