Improving RNA-Seq precision with MapAl

Frontiers in Genetics

Paweł P Łabaj¹  Bryan E Linggi²  H Steven eWiley²  David P Kreil³ 

[1] Boku University Vienna;Pacific Northwest National Laboratory;University of Warwick;

关键词: Gene Expression Profiling;    RNA-Seq;    Reliability;    Transcriptomics;    measurement precision;    read mapping;   

DOI  :  10.3389/fgene.2012.00028

来源: DOAJ

【 摘 要 】

With currently available RNA-Seq pipelines, expression estimates for most genes are very noisy. We here introduce MapAl, a tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. In the post-processing of RNA-Seq reads, it incorporates gene models already at the stage of read alignment, increasing the number of reliably measured known transcripts consistently by 50%. Adding genes identified de-novo then allows a reliable assessment of double the total number of transcripts compared to other available pipelines. This substantial improvement is of general relevance: Measurement precision determines the power of any analysis to reliably identify significant signals, such as in screens for differential expression, independent of whether the experimental design incorporates replicates or not.

【 授权许可】

Unknown