Improving RNA-Seq Precision with MapAl

Łabaj, Paweł P.; Linggi, Bryan E.; Wiley, H. Steven; Kreil, David P.

doi:10.3389/fgene.2012.00028

Improving RNA-Seq Precision with MapAl

Journal Article · Mon Apr 02 00:00:00 EDT 2012 · Frontiers in Genetics

DOI:https://doi.org/10.3389/fgene.2012.00028· OSTI ID:1629070

Łabaj, Paweł P. ^[1]; Linggi, Bryan E. ^[2]; Wiley, H. Steven ^[2]; Kreil, David P. ^[3]

Boku Univ. Vienna (Austria). Dept. of Biotechnology; DOE/OSTI
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab.
Boku Univ. Vienna (Austria). Dept. of Biotechnology; Univ. of Warwick, Coventry (United Kingdom). School of Life Sciences

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.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1629070

Journal Information:: Frontiers in Genetics, Journal Name: Frontiers in Genetics Vol. 3; ISSN 1664-8021

Publisher:: Frontiers Media S.A.Copyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
RNA-Seq
gene expression profiling
measurement precision
read mapping
reliability
splice-form discrimination
transcriptomics

Improving RNA-Seq Precision with MapAl

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References (19)

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