Please refer to the Altrans manual where the method is annotated in more detail and examples of how to run Altrans are provided. The program also allows the user to calculate an F value from all the links that a primary exon makes regardless of the direction. Along with the F values, the raw link counts are also outputted, which allow filtering of results eliminating low count links. These raw counts can also be normalized and subsequently reread by the program to calculate the F values. Memory usage and speed heavily depend on the complexity of the annotation and the number of reads in the alignment file. For a sample alignment with 50 million reads and an annotation with 539,748 unique exons, Altrans ran for 20 min and consumed 784 MB of RAM on a single 2.2 GHz core under Linux.