Hi all,
I recently did a ChIP seq assay and when I did the analysis I only lost 10% of the reads in my IP. Previously coworkers have done a similar ChIP-seq and they lost about 90% of the reads. My understanding is that duplicate reads from ChIP-seq tend to be PCR amplification bias and thus having low duplication levels is a good thing. The problem is that the ChIP with only 10% unique reads shows the expected change in binding in control vs treatment and the one with 90% of unique reads doesn't show any change. Has anyone encountered this before? Or have a any ideas?
I recently did a ChIP seq assay and when I did the analysis I only lost 10% of the reads in my IP. Previously coworkers have done a similar ChIP-seq and they lost about 90% of the reads. My understanding is that duplicate reads from ChIP-seq tend to be PCR amplification bias and thus having low duplication levels is a good thing. The problem is that the ChIP with only 10% unique reads shows the expected change in binding in control vs treatment and the one with 90% of unique reads doesn't show any change. Has anyone encountered this before? Or have a any ideas?
Comment