Tools and best practices for retrotransposon analysis using high-throughput sequencing data

• DOI: 10.1186/s13100-019-0192-1
• Publication Date: 2019-12-29T10:02:28Z
• Authors: Aurélie Teissandier; Nicolas Servant; Emmanuel Barillot; Deborah Bourc’his
• Keywords: Retrotransposon

Sequencing technologies give access to a precise picture of the molecular mechanisms acting upon genome regulation. One biggest technical challenges with sequencing data is map millions reads reference genome. This problem exacerbated when dealing repetitive sequences such as transposable elements that occupy half mammalian mass. Sequenced coming from these regions introduce ambiguities in mapping step. Therefore, applying dedicated parameters and algorithms has be taken into consideration regulation investigated datasets.Here, we used simulated on mouse human genomes define best for aligning element-derived The efficiency most commonly aligners was compared further evaluated how element representation should estimated using available methods. mappability different transposon families calculated giving an overview their evolution.Based data, provided recommendations alignment quantification steps performed expression or studied, identified limits detecting specific young genomes. These principles may help community adopt standard procedures raise awareness difficulties encountered study elements.