What you can do is to use a peak caller between the two files. You will do this twice, once to find enriched regions in one file that are not in the other and viceversa. MACS is one of the tools that will do the job. You just need to convert your SAM files to BAM.
Normally, peak callers try to find the enriched genomic regions of a sample, but since the distrubution of reads is not homogeneous througout the genome they use a so called input file to distinguish spurious enrichments from real enrichments. In other words, peak callers assess enrichments given a background signal. However, you can replace this background signal for comparison with another comparable sample (based in the same genome assembly) that is not an input. In that case the peak caller will identify enrichments that are statistically significant in one of the samples with respect to the other sample.