I have ChIP-seq samples with replicates for the same experiment. I have processed ChIP-seq as follows,
- Bowtie and Bowtie2 (50 bp read length, used both outputs for further processing)
- picard (duplicate removal)
- NGSUtils (BAMutils, clean with Black list and MAPQ 30)
- Deeptools (fingerprint, BAMsummary and correlation)
I am planning to do peak calling using this replicate samples (2 x treatment and 2 x Input) with MACS2. But when I check the correlation (pearson) between Input replicate samples (S1), it gives 0.61 (highlighted with box) unlike in treatment replicates it was above 0.85 [refer attached figure below].
Is it fine to consider S1_InputR1 and S1_InputR2 as replicates when doing peak calling with MACS2 ? [refer attached figure below]
Please give some suggestion.