At first I was skeptical that there was very little documentation, and things got worse when my jobs produced an empty results file without any error messages to troubleshoot the issues. Then I took a close look at the supplied test files and tried to match the format completely and then finally got it to work. Generating the "map.txt" file took a while and I don't see why the mireap can't directly use sam files. I must say the results are absolutely worth the effort in generating the "map.txt" file and troubleshooting other issues. The output files show regions of the genome which express microRNA that we can now test with PCR. With more documentation and helpful error messages, this software could be really good.