Hi,
I did chip-seq on a histone modification of treated cells and untreated cells, I expect to receive more fragments at the treated fraction and less at the untreated one. But for the sequencing the same concentration of DNA is used that neutralizes differences between the fractions. For example, in the bioanalyzer one sample was 4 times higher in treated then untreated, but I didn’t saw this different in the results of MACS2. So, how can I overcome it with bioinformatics tools?
Thanks,
I did chip-seq on a histone modification of treated cells and untreated cells, I expect to receive more fragments at the treated fraction and less at the untreated one. But for the sequencing the same concentration of DNA is used that neutralizes differences between the fractions. For example, in the bioanalyzer one sample was 4 times higher in treated then untreated, but I didn’t saw this different in the results of MACS2. So, how can I overcome it with bioinformatics tools?
Thanks,
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