ChIP-seq vs. RNA-seq
1 answer
Map them both to a reference; the RNA-seq library will be more likely to have splice junctions (look for "N" in the BAM cigar string) and will be sparse in intergenic regions, while the ChIP-seq will have more even coverage, less dynamic range, and will probably have some low-level signal in most places. If it's a decent ChIP experiment, you'll see clear punctate peaks (if it's from transcription factors) or broad domains (from e.g., histone modification ChIP).
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A similar question was recently asked: Characteristic features of Chip-seq and RNA-seq data
Take a look at the answers there. This sort of thing should not be happening in the first place. In case this is a test of some sort then we should not be helping you anyway :)