rna-seq mapping and detection of gene fusions with a suffix array algorithmrna-seq映射和检测的基因融合后缀数组的算法.pdfVIP

RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm 1 1 2 1 1 1 Onur Sakarya *, Heinz Breu , Milan Radovich , Yongzhi Chen , Yulei N. Wang , Catalin Barbacioru , 1 3 3 1 1 1 Sowmi Utiramerur , Penn P. Whitley , Joel P. Brockman , Paolo Vatta , Zheng Zhang , Liviu Popescu , 1 1 1 1 1 1 Matthew W. Muller , Vidya Kudlingar , Nriti Garg , Chieh-Yuan Li , Benjamin S. Kong , John P. Bodeau , 1 3 3 1 1 1 Robert C. Nutter , Jian Gu , Kelli S. Bramlett , Jeffrey K. Ichikawa , Fiona C. Hyland *, Asim S. Siddiqui * 1 Life Technologies, Foster City, California, United States of America, 2 Indiana University School of Medicine, Indianapolis, Indiana, United States of America, 3 Life Technologies (Ambion), Austin, Texas, United States of America Abstract High-throughput RNA sequencing enables quantification of transcripts (both known and novel), exon/exon junctions and fusions of exons from different genes. Discovery of gene fusions–particularly those expressed with low abundance– is a challenge with short- and medium-length sequencing reads. To address this challenge, we implemented an RNA-Seq mapping pipeline within the LifeScope software. We introduced new features including filter and junction mapping, annotation-aided pairing rescue and accurate mapping qualit