Integrate chip-seq with rna-seq?

Question

[Tonkatsu]

How would one go about associating Chip-seq data (from encode) with rna-seq differentially expressed genelists? In particular, whether certain differentially expressed genes are associated with certain transcription factor binding elements. Is it possible to natively do this in encode (I am having some trouble interpreting the layout) or some other program? Thanks

[cpad0112]

http://cistrome.org/BETA/

[nihilior]

Supposing you have one file with annotated peaks (for example peaks called with macs2 and annotated with ChIPSeeker R package) and one file with differential expression data from DeSeq you can a merge with Python on common columns (for example on gene name or ensembl gene ID) and then do enrichment analysis on the resulting file.