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FANSe2: A Robust Tool for Quantitative NGS Applications

FANSe2: A Robust Tool for Quantitative NGS Applications

Correct and bias-free interpretation of the deep sequencing data is inevitably dependent on the complete mapping of all mappable reads to the reference sequence, especially for quantitative RNA-seq applications. Seed-based algorithms are generally slow but robust, while Burrows-Wheeler Transform (BWT) ...

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Hobbes2 – for fast and accurate alignment of NGS reads

Hobbes2 – for fast and accurate alignment of NGS reads

Next-generation sequencing (NGS) enables rapid production of billions of bases at a relatively low cost. Mapping reads from next-generation sequencers to a given reference genome is an important first step in many sequencing applications. Popular read mappers, such as Bowtie ...

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Is trimming beneficial in RNA-Seq??

Is trimming beneficial in RNA-Seq??

by  Matthew MacManes I was pointed to a new paper in PLOS ONE: An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis. Their central thesis seems to be this: “….trimming is beneficial in RNA-Seq, SNP identification and genome ...

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PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution

PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution

Correctly estimating isoform-specific gene expression is important for understanding complicated biological mechanisms and for mapping disease susceptibility genes. However, estimating isoform-specific gene expression is challenging because various biases present in RNA-Seq (RNA sequencing) data complicate the analysis, and if not ...

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