Article
Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 Genomes data.
PloS one - 1 Jan 2013
Quinn Emma M, Cormican Paul, Kenny Elaine M, Hill Matthew, Anney Richard, Gill Michael, Corvin Aiden P, Morris Derek W
Abstract excerpt
Next-generation RNA sequencing (RNA-seq) maps and analyzes transcriptomes and generates data on sequence variation in expressed genes. There are few reported studies on analysis strategies to maximize the yield of quality RNA-seq SNP data. We evaluated the performance of different SNP-calling methods following alignment to both genome and transcriptome by applying them to RNA-seq data from a HapMap lymphoblastoid...
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