The enormous technological progress in the field of functional genomics during the last 15 years had a significant impact on animal sciences. With the development of Next Generation Sequencing it became feasible to analyze genomes and transcriptomes within short time frames and affordable costs. One major challenge of this rapid development is to manage the data flood and to perform data analysis and integration in an optimal manner. This review provides some information about a typical analysis pipeline for RNASequencing (RNA-Seq) data and a strategy for the analysis of small RNA-Seq data derived from species with poor annotation for non-coding RNA genes. Furthermore, problems regarding gene annotation in livestock species and their possible implications for data analysis and interpretation are discussed. Despite of not yet solved problems and challenges with respect to data analysis and integration the approaches in the field of functional genome analysis opened up new ways to try to understand the complex trait fertility.