How to decide the parameters and parameter values when running ChIP-seq Peak Calling for H3K27ac data in MACS?

Question

[mudithekanayake]

I have alignment data in SAM files from ChIP-seq analysis for H3K27ac mark. I need to call peaks using MACS2. But I'm having issues with selecting parameters and values of the parameters. I will be really grateful if someone can help me figuring out this issue. Thank you. Mudith

[Gjain]

What issues are you facing?

[jared.andrews07]

This depends to some degree on your data quality. You can play with the q value cutoff, min length or using --broad (if you are getting very focal peaks), or changing the m thresholds. It really depends on what you're facing. Generally, playing with things until some obvious regions pass the eye test and are actually called as reasonable peaks is usually enough.

[ATpoint]

Hello mudithekanayake!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/11317/how-to-decide-the-parameters-and-parameter-values-when-running-chip-seq-peak-cal

This is typically not recommended as it runs the risk of annoying people in both communities.

Answer 1

[mark.ziemann]

Start with the default parameters. Make sure you supply an input sample. If you don't get many or any peaks it could be that the ChIP enrichment hasn't worked and you would need to look at ways to make it more specific. eg: more extensive wash steps, or trying another antibody. Please give it a try and tell us whether you run into issues/errors