Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees.

We found that the presence of RNA pol II ChIP-seq peaks had a small but highly significant correlation with transcript abundance measured by RNA-seq (R 2 = 0.07, F 1,41333 = 3254; p-val<2.2x10 -16 ), as shown in Figure 6 , transcript levels were significantly higher when comparing the population of genes having a peak within 500bp of their TSS to the population of genes without such a peak.

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