What are the characteristic features of Chip-seq and RNA-seq data? If I have fastq files which are the results of Chip-seq and RNA-seq experiment is it possible to differentiate then, for example by comparing to Chip-seq input result, which is explicitly marked?

**RNA-seq** : (In eukaryots) splicing (some reads must be split to map), very uneven read coverage, especially in total RNA-seq where rRNA reads dominate.

**ChIP-seq** : relatively even coverage in the input fraction.

To check genome coverage requires mapping, but over-represented sequences can be analysed with [fastqc][1] and blast to provide a quick indication directly from the fastq files : If there are over-represented sequences that corresponds to highly expressed genes, then you are dealing with RNA-seq data.

  [1]: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/