Accuracy of allele frequency estimation using pooled RNA-Seq (Q35015999)

5 August 2017

Accuracy of allele frequency estimation using pooled RNA-Seq (English)

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5 August 2017

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M Konczal

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Wiesław Babik

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W Babik

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Jacek Radwan

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J Radwan

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Paweł Koteja

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P Koteja

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author name string

M T Stuglik

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5 August 2017

16 November 2013

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Molecular Ecology Resources

5 August 2017

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5 August 2017

14

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5 August 2017

381-392

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5 August 2017

2

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vipR: variant identification in pooled DNA using R.

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Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate

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A statistical method for the detection of variants from next-generation resequencing of DNA pools

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Statistical analysis strategies for association studies involving rare variants

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Evaluation of next-generation sequencing software in mapping and assembly

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Identification of the sources of error in allele frequency estimations from pooled DNA indicates an optimal experimental design

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Epistasis as the primary factor in molecular evolution

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The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis

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Quantification of rare allelic variants from pooled genomic DNA

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Assemblathon 1: a competitive assessment of de novo short read assembly methods

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UCHIME improves sensitivity and speed of chimera detection

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The next generation of molecular markers from massively parallel sequencing of pooled DNA samples

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Global patterns of cis variation in human cells revealed by high-density allelic expression analysis

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Characterizing natural variation using next-generation sequencing technologies.

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A hierarchical Bayesian model for next-generation population genomics

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Full-length transcriptome assembly from RNA-Seq data without a reference genome

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Evaluation of allele frequency estimation using pooled sequencing data simulation.

21 January 2018

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CAP3: A DNA sequence assembly program

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The genomic basis of adaptive evolution in threespine sticklebacks

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VarScan: variant detection in massively parallel sequencing of individual and pooled samples

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PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

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Fast gapped-read alignment with Bowtie 2

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A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

21 January 2018

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Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

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The Sequence Alignment/Map format and SAMtools

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Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

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Resurrecting the role of transcription factor change in developmental evolution.

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Next-generation transcriptome assembly

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Negative frequency-dependent selection of sexually antagonistic alleles in Myodes glareolus.

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Genetic analysis of genome-wide variation in human gene expression

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Mapping and quantifying mammalian transcriptomes by RNA-Seq

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The genomics of adaptation.

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Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing

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Genetic history of an archaic hominin group from Denisova Cave in Siberia

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A guide to the genomics of ecological speciation in natural animal populations.

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A scaling normalization method for differential expression analysis of RNA-seq data

21 January 2018

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Laboratory model of adaptive radiation: a selection experiment in the bank vole

21 January 2018

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RNA-Seq identifies SNP markers for growth traits in rainbow trout

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Regional and strain-specific gene expression mapping in the adult mouse brain

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Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression

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DNA Pooling: a tool for large-scale association studies

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De novo transcriptomic analyses for non-model organisms: an evaluation of methods across a multi-species data set.

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A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

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Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection

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Contrasting patterns of diversity and population differentiation at the innate immunity gene toll-like receptor 2 (TLR2) in two sympatric rodent species.

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Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing.

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Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments

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Neutral and adaptive variation in gene expression

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Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow

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Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster

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The evolutionary landscape of alternative splicing in vertebrate species

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21 January 2018

Identifiers

DOI

10.1111/1755-0998.12186

1 reference

5 August 2017

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PubMed ID

24119300