Unspliced Mapping Tools

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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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ContextMap – Mining RNA-Seq Data for Infections and Contaminations

RNA sequencing (RNA–seq) provides novel opportunities for transcriptomic studies at nucleotide resolution, including transcriptomics of viruses or microbes infecting a cell. However, standard approaches for mapping the resulting sequencing reads generally ignore alternative sources of expression other than the host ...

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