I am looking at a ChIP-seq data set where, for one of the suspected target genes, we see a coverage profile that looks suspiciously like RNA-seq data, i.e. the reads are lining up very regularly along the exons as opposed to the usual peaky profile that one would expect in ChIP-seq. On further inspection, we also find that using TopHat, we find a handful of spliced alignments joining the same two exons in the gene. (Initially we had used a different aligner; this was just for checking the potential artifact I am describing.)
Now, I have heard of genomic DNA contamination in RNA-seq libraries, but I have a harder time figuring out how one can get RNA (or rather cDNA, I suppose) contamination in a ChIP-seq library. Any ideas where this might come from?