Hi, I would to ask to everyone that had experience with ChIP seq data So, here I have different time point samples (1h, 2h, 4h, 8h, and 24h) those samples came from 2 different batches, each of the time point samples have 3 replications with treated TF and 3 replication untreated TF (EtOH). And 1 single input from the batch 2 only.
The approach to analyse the binding sites, I used csaw package, and I was doing contrast between treated and untreated samples for each time point
Now, I want to also analyse the binding sites in untreated samples, I asked chat GPT how to approach this, and it suggested by using input, to do the contrast for each time point of untreated samples and with one single input.
The question is does this approach make sense and reliable enough for analysing binding sites in untreated samples? Or do you have any suggestion how to do it
Thank you so much, any thoughts will be appreciated. Thank you and have a nice day
Ignore the input -- it is only used for peak calling but not differential analysis. The comparison between untreated is technically the same as for the treated. So you tell edgeR (that is what csaw is using under the hood) to contrast the untreated samples. I see nothing unusual here. For more help try to ask y technically more precise question with details.
hello thank you for your reply, can you clarify how to do the contrast for the untreated samples? here, what I would like to achieve is to know the binding sites that exist in my untreated samples in each time point,
correct me if I am wrong
for example to know the list significant binding sites in untreated sample 1 hour, this is the approach how to solve it :
contrast_EtOh_1h <- makeContrasts (Untreated.EtOh.1h - Treated.1h, levels =design)