-Automatic preprocessing of annotation files added (only accepted formats). -Ability to reduce the investigation to one chromosome or one region added. -The user can now decide if novel isoforms are detected. -We provide clear examples of what formats are acceptable by iReckon. -We provide pre-processed hg19 annotations (in Example files). Bug fixes/catches: -Errors because of wrong annotation format are better catched. -Gene names reporting is improved in output. -Bug when writing transcriptome fixed. -Bug when parsing BWA result ("Bad read alignment") fixed. -Bug when the output directory specified do not end with '/' fixed. -Clearer separation between error messages and warnings. -Several error messages have been improved/added.