Tag Archives: read mapping

from On Biology by Fritz Sedlazeck Read mapping is the process of aligning short sequences (also known as ‘reads’) to a reference genome or a de novo assembly. It is a major analysis step in nearly every Next Generation Sequencing ...

from RoBlog by Rob Patro – Thoughts and musings on science and life Introducing RapMap I’ve recently been working with my student Avi Srivastava on a new project, RapMap.  RapMap is a tool for mapping (see below for the distinction between mapping ...

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 researchers from the University of Chicago and Stanford University describe WASP, a suite ...

Accurate identification of genetic variants such as single nucleotide polymorphisms (SNPs) or RNA editing sites from RNA-Seq reads is important, yet challenging, because it necessitates a very low false positive rate in read mapping. Although many read aligners are available, ...

Recent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. Researchers at the University of Vienna present ViennaNGS, an integrated collection of Perl modules ...

University of Notre Dame – College of Science Time: Mon May 4, 2015, 4:15PM – 5:15PM Location: 127 Hayes-Healy Center Hui Jiang Department of Biostatistics University of Michigan Statistical modeling of RNA sequencing data Ultra high-throughput sequencing of transcriptomes (RNA-Seq) ...

Mapping of short sequencing reads is a crucial step in the analysis of RNA sequencing (RNA-seq) data. ContextMap is an RNA-seq mapping algorithm that uses a context-based approach to identify the best alignment for each read and allows parallel mapping ...

One of the major mechanisms of generating mRNA diversity is alternative splicing, a regulated process that allows for the flexibility of producing functionally different proteins from the same genomic sequences. This process is often altered in cancer cells to produce ...

RNA-Seq has become increasingly popular in transcriptome profiling. One aspect of transcriptome research is to quantify the expression levels of genomic elements, such as genes, their transcripts and exons. Acquiring a transcriptome expression profile requires genomic elements to be defined ...

Here, researchers at ecSeq Bioinformatics provide detailed performance comparisons of NGS read aligners. They stress that benchmarks only measure specific aspects and may not be used to claim any universal superiority or inferiority of a particular tool. In order to ...