Hi all (again)
If I have a sample that we have both ChIP-seq and RNA-seq data on (just one replicate of each so far), is there a way to integrate the data from the 2 techniques? More specifically, for the sample, we didn't do a treatment or a knockdown or anything for either technique meaning that I'm not going to have "differential expression" of my RNA-seq data. Just expression counts. All the tools I've seen so far (such as BETA etc) need some sort of fold change and stats for the RNA-seq data and I don't have that. Is there anything I can do or just do a really basic analysis such as ranking my RNA-seq transcripts and taking those that are the most highly expressed and seeing how many of them have a ChIP-seq peak within a arbitrary distance from the TSS?
And yes, poor experiment design, lack of replicates (so far) etc etc but that's out of my hands right now. I've just got the data and have been asked to do what I can with it.