WASP: allele-specific software for robust molecular quantitative trait locus discovery
Open Access
- 14 September 2015
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Methods
- Vol. 12 (11), 1061-1063
- https://doi.org/10.1038/nmeth.3582
Abstract
The WASP suite of open-source tools performs unbiased allele-specific sequence read mapping and provides improved power for molecular QTL discovery. Allele-specific sequencing reads provide a powerful signal for identifying molecular quantitative trait loci (QTLs), but they are challenging to analyze and are prone to technical artifacts. Here we describe WASP, a suite of tools for unbiased allele-specific read mapping and discovery of molecular QTLs. Using simulated reads, RNA-seq reads and chromatin immunoprecipitation sequencing (ChIP-seq) reads, we demonstrate that WASP has a low error rate and is far more powerful than existing QTL-mapping approaches.Keywords
This publication has 19 references indexed in Scilit:
- DNase I sensitivity QTLs are a major determinant of human expression variationNature, 2012
- A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq dataGenome Research, 2011
- Haplotype and isoform specific expression estimation using multi-mapping RNA-seq readsGenome Biology, 2011
- AlleleSeq: analysis of allele‐specific expression and binding in a network frameworkMolecular Systems Biology, 2011
- Analysis and design of RNA sequencing experiments for identifying isoform regulationNature Methods, 2010
- Differential expression analysis for sequence count dataGenome Biology, 2010
- Transcriptome genetics using second generation sequencing in a Caucasian populationNature, 2010
- Understanding mechanisms underlying human gene expression variation with RNA sequencingNature, 2010
- Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing dataBioinformatics, 2009
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009