compare the background levels in two chip-seq experiments
Dear all,
which algorithms would you recommend in order to assess the background levels between two ChIP-seq experiments ?
Thanks,
Bogdan
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It might depend a little on what you consider background, this could refer to background signal in the IP sample, or background peaks found in the input (whole cell extract) sample. However, there are a few common ways to assess differences in samples.
- You could examine the Fraction of Reads in Peaks (Landt et al, Genome Research Sept. 2012, 22(9): 1813–1831).
- You could examine the Irreproducible Discovery Rate (also mentioned in Landt et al.)
- Depending on how you found your peaks, if you used MACS for instance, you could examine the distribution of P or Q-Values of the peaks. Different levels of background would give rise to different distributions for your peaks, as well as comparing the fold enrichment values for each peak set.
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