To align sample files to the peak identification reference file, you use the same general procedure as when you are aligning sample files to the whole genome reference with one notable exception—you must use the .fasta file created from the Peak Identification report, which contains only the peak regions, as the reference file. After NextGENe completes the alignment of the sample files to the peak identification reference file, the results are shown in the NextGENe Viewer, which provides a graphic representation of expression levels for each region. Red lines indicate region boundaries. Sequence reads that align with each region are shown beneath where they align. Gray bars indicate coverage (expression level).