I am trying to find some resources that discuss how to best prepare ChIP-seq data to be processed in DESeq2. I am having trouble determining how to best go about preparing a count matrix to be used for generating a DESeqDataSet. I have .bam files from and corresponding .narrowPeak files, but I am not sure how to appropriately generate a count matrix from these data or something that can serve as input for DESeq2. I have done some googling and reading, but have been unable to find a clear explanation.
If you are aware or could share any good tutorials out there about how to go about setting up ChIP-seq data for DESeq2 analysis that would be great!
Any assistance is appreciated!