I want to include differential binding of H3K27ac (ChIP-Seq) near genes in my differential gene expression (RNA-seq) analysis. The aim of this analysis is to see the expression dynamics in a cellline between 3 time points (proliferating (day 0) and differentiation (day 1.5 and 3)). I want to see for which genes the expression pattern correlates with the H3K27ac binding near these genes. For example gene X is not expressed at day 0 but is highly expressed at day 1.5 and 3. I want to know if there is a strong H3K27ac signal near this gene at day 1.5 and 3 and not at day0.
For the differential gene expression I used DESeq2 and for the ChIP-Seq I was planning to do the same (using DEseq to find genes with differential H3K27ac binding), and then later check for genes with correlating patterns. The thing is that for the RNA seq I used STAR to create the readcount files. I can create the readcount files for H3K27ac with htseq-count but I'm doubting if this is the right way to do this (comparing readcounts obtained with 2 different methods).
Would this be the right way to do this? And if not, could anyone give some advice on how to do it right, maybe there are better tools to do this or something that can do this all at once. I'm a beginning researcher without that much experience in this sort of analysis so any input would be highly appreciated.
Thanks in advance.