I just received sequences from the first ChIP seq experiment done in my lab. I run triplicates for the samples and used input as a control. I started the analysis with UseGalaxy and already have some problems after FastQC step!! I found high level of duplicated read in my samples (input are fines) with only 4% of seqs remaining if deduplicated.
Is it worth making the analysis after removing the duplicates? I was considering removing the duplicated read and combining single reads from the triplicates.
many thanks for any help!